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Sample records for g-rich short tandem

  1. Short G-rich oligonucleotides as a potential therapeutic for Huntington's Disease

    PubMed Central

    Skogen, Michael; Roth, Jennifer; Yerkes, Sarah; Parekh-Olmedo, Hetal; Kmiec, Eric

    2006-01-01

    Background Huntington's Disease (HD) is an inherited autosomal dominant genetic disorder in which neuronal tissue degenerates. The pathogenesis of the disease appears to center on the development of protein aggregates that arise initially from the misfolding of the mutant HD protein. Mutant huntingtin (Htt) is produced by HD genes that contain an increased number of glutamine codons within the first exon and this expansion leads to the production of a protein that misfolds. Recent studies suggest that mutant Htt can nucleate protein aggregation and interfere with a multitude of normal cellular functions. Results As such, efforts to find a therapy for HD have focused on agents that disrupt or block the mutant Htt aggregation pathway. Here, we report that short guanosine monotonic oligonucleotides capable of adopting a G-quartet structure, are effective inhibitors of aggregation. By utilizing a biochemical/immunoblotting assay as an initial screen, we identified a 20-mer, all G-oligonucleotide (HDG) as an active molecule. Subsequent testing in a cell-based assay revealed that HDG was an effective inhibitor of aggregation of a fusion protein, comprised of a mutant Htt fragment and green fluorescent protein (eGFP). Taken together, our results suggest that a monotonic G-oligonucleotide, capable of adopting a G-quartet conformation is an effective inhibitor of aggregation. This oligonucleotide can also enable cell survival in PC12 cells overexpressing a mutant Htt fragment fusion gene. Conclusion Single-stranded DNA oligonucleotides capable of forming stable G-quartets can inhibit aggregation of the mutant Htt fragment protein. This activity maybe an important part of the pathogenecity of Huntington's Disease. Our results reveal a new class of agents that could be developed as a therapeutic approach for Huntington's Disease. PMID:17014717

  2. Mechanistic insights into human pre-mRNA splicing of human ultra-short introns: potential unusual mechanism identifies G-rich introns.

    PubMed

    Sasaki-Haraguchi, Noriko; Shimada, Makoto K; Taniguchi, Ichiro; Ohno, Mutsuhito; Mayeda, Akila

    2012-06-29

    It is unknown how very short introns (<65 nt; termed 'ultra-short' introns) could be spliced in a massive spliceosome (>2.7 MDa) without steric hindrance. By screening an annotated human transcriptome database (H-InvDB), we identified three model ultra-short introns: the 56-nt intron in the HNRNPH1 (hnRNP H1) gene, the 49-nt intron in the NDOR1 (NADPH dependent diflavin oxidoreductase 1) gene, and the 43-nt intron in the ESRP2 (epithelial splicing regulatory protein 2) gene. We verified that these endogenous ultra-short introns are spliced, and also recapitulated this in cultured cells transfected with the corresponding mini-genes. The splicing of these ultra-short introns was repressed by a splicing inhibitor, spliceostatin A, suggesting that SF3b (a U2 snRNP component) is involved in their splicing processes. The 56-nt intron containing a pyrimidine-rich tract was spliced out in a lariat form, and this splicing was inhibited by the disruption of U1, U2, or U4 snRNA. In contrast, the 49- and 43-nt introns were purine-rich overall without any pyrimidine-rich tract, and these lariat RNAs were not detectable. Remarkably, shared G-rich intronic sequences in the 49- and 43-nt introns were required for their splicing, suggesting that these ultra-short introns may recruit a novel auxiliary splicing mechanism linked to G-rich intronic splicing enhancers.

  3. Short Tandem Repeat DNA Internet Database

    National Institute of Standards and Technology Data Gateway

    SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

  4. Fully integrated, fully automated generation of short tandem repeat profiles

    PubMed Central

    2013-01-01

    Background The generation of short tandem repeat profiles, also referred to as ‘DNA typing,’ is not currently performed outside the laboratory because the process requires highly skilled technical operators and a controlled laboratory environment and infrastructure with several specialized instruments. The goal of this work was to develop a fully integrated system for the automated generation of short tandem repeat profiles from buccal swab samples, to improve forensic laboratory process flow as well as to enable short tandem repeat profile generation to be performed in police stations and in field-forward military, intelligence, and homeland security settings. Results An integrated system was developed consisting of an injection-molded microfluidic BioChipSet cassette, a ruggedized instrument, and expert system software. For each of five buccal swabs, the system purifies DNA using guanidinium-based lysis and silica binding, amplifies 15 short tandem repeat loci and the amelogenin locus, electrophoretically separates the resulting amplicons, and generates a profile. No operator processing of the samples is required, and the time from swab insertion to profile generation is 84 minutes. All required reagents are contained within the BioChipSet cassette; these consist of a lyophilized polymerase chain reaction mix and liquids for purification and electrophoretic separation. Profiles obtained from fully automated runs demonstrate that the integrated system generates concordant short tandem repeat profiles. The system exhibits single-base resolution from 100 to greater than 500 bases, with inter-run precision with a standard deviation of ±0.05 - 0.10 bases for most alleles. The reagents are stable for at least 6 months at 22°C, and the instrument has been designed and tested to Military Standard 810F for shock and vibration ruggedization. A nontechnical user can operate the system within or outside the laboratory. Conclusions The integrated system represents the

  5. Short-pulse CO₂ laser with longitudinal tandem discharge tube.

    PubMed

    Uno, K; Akitsu, T; Jitsuno, T

    2014-10-01

    We developed a longitudinally excited CO2 laser with a tandem discharge tube. The tandem scheme was constituted of two 30-cm long discharge tubes connected with an intermediate electrode. Two parts, each consisting of a charged capacitance and a 30-cm long discharge tube, were electrically connected in parallel and switched by a spark gap. The tandem scheme produced a short laser pulse like that of a TEA-CO2 laser with a charging voltage of -24.8 kV, which was smaller than the -40.0 kV charging voltage of our previous CO2 laser. At a gas pressure of 3.8 kPa, the spike pulse width was 145 ns, the pulse tail length was 58.8 μs, the output energy was 52.0 mJ, and the spike pulse energy was 2.4 mJ. We also investigated the dependence of the laser pulse and the discharge voltage on gas pressure.

  6. Mutational dynamics of short tandem repeats in human genome

    NASA Astrophysics Data System (ADS)

    Borstnik, B.; Pumpernik, D.

    2004-01-01

    The evolutionary dynamics of short tandem repeats of nucleotide sequences of the human genome is studied. It is shown that a model due to which the evolutionary repeat dynamics consists of elongations and shortenings of the repeats, combined with point mutations, is degenerate in the sense that an ambiguity exists regarding the role of point mutations and slippage asymmetry. By introducing a measure of the correlations between the positions of the repeats along the DNA sequences we were able to remove the degeneracy and to show that the slippage events which are the main factor in repeat evolution exhibit more frequent shortenings than elongations.

  7. Analysis of Short Tandem Repeats by Parallel DNA Threading

    PubMed Central

    Zajac, Pawel; Öberg, Christine; Ahmadian, Afshin

    2009-01-01

    The majority of studies employing short tandem repeats (STRs) require investigation of several of these genetic markers. As such, we demonstrate the feasibility of the trinucleotide threading (TnT) approach for scalable analysis of STRs. The TnT method represents a parallel amplification alternative that addresses the obstacles associated with multiplex PCR. In this study, analysis of the STR fragments was performed with capillary gel electrophoresis; however, it should be possible to combine our approach with the massive 454 sequencing platform to considerably increase the number of targeted STRs. PMID:19915680

  8. Short-tandem repeat analysis in seven Chinese regional populations

    PubMed Central

    2010-01-01

    In the present study, we investigated the application of 13 short tandem repeat (STR) loci (D13S317, D7S820, TH01, D16S539, CSFIPO, VWA, D8S1179, TPOX, FGA, D3S1358, D21S11, D18S51 and D5S818) routinely used in forensic analysis, for delineating population relationships among seven human populations representing the two major geographic groups, namely the southern and northern Chinese. The resulting single topology revealed pronounced geographic and population partitioning, consistent with the differences in geographic location, languages and eating habits. These findings suggest that forensic STR loci might be particularly powerful tools in providing the necessary fine resolution for reconstructing recent human evolutionary history. PMID:21637565

  9. Systematic Profiling of Short Tandem Repeats in the Cattle Genome.

    PubMed

    Xu, Lingyang; Haasl, Ryan J; Sun, Jiajie; Zhou, Yang; Bickhart, Derek M; Li, Junya; Song, Jiuzhou; Sonstegard, Tad S; Van Tassell, Curtis P; Lewin, Harris A; Liu, George E

    2017-01-01

    Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

  10. Mapping of short tandem repeat polymorphisms on human chromosome 3

    SciTech Connect

    Wilkie, P.J.; Weber, J.L. )

    1994-01-01

    Linkage analysis was used to determine map positions for 18 short tandem repeat polymorphisms that continuously span 186 cM of human chromosome 3. Mapping was based on the genotyping of 40 CEPH reference families. Loci order from pter-qter was D3S1252-D3S1235-D3S1234-D3S1233-D3S1254-D3S1251-D3S1215-RHO-ACPP-D3S1238-D3S1206- D3S196-D3S1237-(D3S1253,D3S1439)-D3S1243-D3S1232-SST. Odds against inversion of adjacent markers in all cases were 700:1 or better, except for the marker pair at D3S1253, D3S1439 that was not separated by any recombinants and therefore could not be ordered. Only one gap greater than 25 cM on the sex-equal map was observed. 14 refs., 1 fig., 1 tab.

  11. Systematic Profiling of Short Tandem Repeats in the Cattle Genome

    PubMed Central

    Haasl, Ryan J.; Sun, Jiajie; Zhou, Yang; Bickhart, Derek M.; Li, Junya; Song, Jiuzhou; Sonstegard, Tad S.; Van Tassell, Curtis P.; Lewin, Harris A.

    2017-01-01

    Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection. PMID:28172841

  12. Genomic landscape of CpG rich elements in human.

    PubMed

    Babenko, Vladimir N; Chadaeva, Irina V; Orlov, Yuriy L

    2017-02-07

    The studies on CpG islands (CGI) and Alu elements functions, evolution, and distribution in the genome started since the discovery in nineteen eighties (1981, 1986, correspondingly). Their highly skewed genome wide distribution implies the non-random retrotransposition pattern. Besides CGIs in gene promoters, CGIs clusters were observed in the homeobox gene regions and in the macrosatellites, but the whole picture of their distribution specifics was not grasped. Attempts to identify any causative features upon their (genome wide) distribution, such as the DNA context mediated preferred insertion sites of Alu repeats, have been made to ascribe their clusters location. Recent emergence of high resolution 3D map of human genome allowed segregating the genome into the large scale chromatin domains of naturally observable nuclear subcompartments, or Topologically Associated Domains (TADs), designated by spatial chromatin distribution. We utilized the chromatin map to elucidate relations between large scale chromatin state and CpG rich elements landscape. In the course of analysis it was confirmed that genes, Alu and CGI clusters maintain obvious, albeit different in strength, preference for open chromatin. For the first time it was clearly shown that the clusters density of the Alu and CGIs monotonically depend on the chromatin accessibility rate. In particular, the highest density of these elements is found in A1 euchromatin regions characterized by a high density of small length genes replicating in the early S-phase. It implies that these elements mediate (CGIs) or are a side element (Alus) of chromatin accessibility. We elucidated that both methylated and non-methylated CGIs display the affinity to chromatin accessibility. As a part of comparative genomics section, we elucidated that the dog's genome non-canonical structure, outstanding in mammals for its high CGIs abundance compared to gene number, is explained by the presence of dense tandem CGI extended hotspots

  13. Assessing the fraction of short-distance tandem splice sites under purifying selection.

    PubMed

    Hiller, Michael; Szafranski, Karol; Sinha, Rileen; Huse, Klaus; Nikolajewa, Swetlana; Rosenstiel, Philip; Schreiber, Stefan; Backofen, Rolf; Platzer, Matthias

    2008-04-01

    Many alternative splice events result in subtle mRNA changes, and most of them occur at short-distance tandem donor and acceptor sites. The splicing mechanism of such tandem sites likely involves the stochastic selection of either splice site. While tandem splice events are frequent, it is unknown how many are functionally important. Here, we use phylogenetic conservation to address this question, focusing on tandems with a distance of 3-9 nucleotides. We show that previous contradicting results on whether alternative or constitutive tandem motifs are more conserved between species can be explained by a statistical paradox (Simpson's paradox). Applying methods that take biases into account, we found higher conservation of alternative tandems in mouse, dog, and even chicken, zebrafish, and Fugu genomes. We estimated a lower bound for the number of alternative sites that are under purifying (negative) selection. While the absolute number of conserved tandem motifs decreases with the evolutionary distance, the fraction under selection increases. Interestingly, a number of frameshifting tandems are under selection, suggesting a role in regulating mRNA and protein levels via nonsense-mediated decay (NMD). An analysis of the intronic flanks shows that purifying selection also acts on the intronic sequence. We propose that stochastic splice site selection can be an advantageous mechanism that allows constant splice variant ratios in situations where a deviation in this ratio is deleterious.

  14. Hybrid de novo tandem repeat detection using short and long reads

    PubMed Central

    2015-01-01

    Background As one of the most studied genome rearrangements, tandem repeats have a considerable impact on genetic backgrounds of inherited diseases. Many methods designed for tandem repeat detection on reference sequences obtain high quality results. However, in the case of a de novo context, where no reference sequence is available, tandem repeat detection remains a difficult problem. The short reads obtained with the second-generation sequencing methods are not long enough to span regions that contain long repeats. This length limitation was tackled by the long reads obtained with the third-generation sequencing platforms such as Pacific Biosciences technologies. Nevertheless, the gain on the read length came with a significant increase of the error rate. The main objective of nowadays studies on long reads is to handle the high error rate up to 16%. Methods In this paper we present MixTaR, the first de novo method for tandem repeat detection that combines the high-quality of short reads and the large length of long reads. Our hybrid algorithm uses the set of short reads for tandem repeat pattern detection based on a de Bruijn graph. These patterns are then validated using the long reads, and the tandem repeat sequences are constructed using local greedy assemblies. Results MixTaR is tested with both simulated and real reads from complex organisms. For a complete analysis of its robustness to errors, we use short and long reads with different error rates. The results are then analysed in terms of number of tandem repeats detected and the length of their patterns. Conclusions Our method shows high precision and sensitivity. With low false positive rates even for highly erroneous reads, MixTaR is able to detect accurate tandem repeats with pattern lengths varying within a significant interval. PMID:26399998

  15. Systematic profiling of bovine short tandem repeats using whole genome sequencing data

    USDA-ARS?s Scientific Manuscript database

    Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive motifs of 2–6 base pairs that are abundant in the genomes of pro- and eukaryotic organisms. Using the program lobSTR and whole genome sequencing data, we systematically profiled STR variation in five Holstein cattl...

  16. Turkish population data with the CODIS multiplex short tandem repeat loci.

    PubMed

    Akbasak, B S; Budowle, B; Reeder, D J; Redman, J; Kline, M C

    2001-12-01

    Allele frequencies for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, D18S51, D3S1358, D21S11, D5S818, FGA, D7S820, HUMTH01, D8S1179, TPOX, D13S317, VWA, and D16S539 were determined on 198 Turkish blood samples.

  17. Short-term learning effects of practice during the performance of the tandem Romberg test.

    PubMed

    Diamantopoulos, I I; Clifford, E; Birchall, J P

    2003-08-01

    The tandem Romberg test is possibly the most common static test of postural stability. This study aims to see if practice effects the performance of the tandem Romberg test. Twenty-four subjects were instructed to practice the tandem Romberg test daily for a period of 10 consecutive days, and were tested on five occasions using the sway magnetometry posturographic system. The test was performed with eyes open and eyes closed either on the floor or on foam. Their ability to perform the test for 60 s was used as a pass/fail criterion. With eyes closed, 65% of tandem Romberg tests were successful on hard surface, and 28% on foam. With eyes open, all subjects scored a 'pass'. On hard surface, the mean path length for the first and last day was 371.7 mm (SD 68.56) and 481 mm (SD 145.47) respectively. On foam, it was 506 mm (SD 139) and 530 mm (SD 212). For the 'fail' tandem Romberg tests, the 75th percentile for the time taken for subjects to perform the test on the first and last days were 18.5 and 9 s on floor, and 18 and 37 s on foam respectively. Across all testing sessions and groups, no significant improvement in performance with practice was observed. The absence of improvement in subjects practising the tandem Romberg test indicates a lack of short-term learning effects. The failure rate, however, associated with eye closure, whether on foam or on hard surface, invalidates the use of the tandem Romberg test in assessing postural stability because of its performance variability.

  18. Short-term clinical outcome and dosimetric comparison of tandem and ring versus tandem and ovoids intracavitary applicators

    PubMed Central

    Mourad, Waleed F.; Allbright, Robert; Packianathan, Satyaseelan; Harrell, Leslie M.; Chinchar, Edmund; Nguyen, Alex; Vijayakumar, Srinivasan

    2015-01-01

    Purpose To compare the short-term toxicity and dosimetry of tandem and ring (TR), and tandem and ovoid (TO) applicators in treatment of gynecologic malignancy. Material and methods Following pelvic external beam radiation therapy (EBRT), a total of 52 computed tomography-based plans from 13 patients with cervical cancer (FIGO IB2-IIIB) were evaluated for HDR brachytherapy. Prescription was 7 Gy to the ICRU point A for four weekly fractions. Gastrointestinal and genitourinary toxicities were evaluated. Clinical target volume (CTV) and organs at risk were delineated on CT scans. Bladder, rectum, and sigmoid mean doses and D2cc were calculated. Treatment time and irradiated tissue volume were compared. Percent of CTV receiving 100% (CTV100%) of the prescribed dose as well as the percent of the prescription dose covering 90% of the CTV (D90) were evaluated. Results Gastrointestinal and genitourinary toxicities were not different between TO and TR applicators. No significant differences in the dose to the right and left point A, or the left point B were observed. TO delivered a higher dose to right point B. Organs at risk doses were similar between the two applicators, except mean rectal dose was lower for TO applicator. Overall, TO treats a larger tissue volume than TR. Mean treatment time was shorter for TR. Tumor coverage (D90 and CTV100%) was equivalent between TO and TR applicators. Conclusion Although TO treats a larger tissue volume than TR, short-term toxicities and tumor coverage are similar. Long-term clinical outcomes will be elucidated with longer follow up period. PMID:26207110

  19. Widespread and subtle: alternative splicing at short-distance tandem sites.

    PubMed

    Hiller, Michael; Platzer, Matthias

    2008-05-01

    Alternative splicing at donor or acceptor sites located just a few nucleotides apart is widespread in many species. It results in subtle changes in the transcripts and often in the encoded proteins. Several of these tandem splice events contribute to the repertoire of functionally different proteins, whereas many are neutral or deleterious. Remarkably, some of the functional events are differentially spliced in tissues or developmental stages, whereas others exhibit constant splicing ratios, indicating that function is not always associated with differential splicing. Stochastic splice site selection seems to play a major role in these processes. Here, we review recent progress in understanding functional and evolutionary aspects as well as the mechanism of splicing at short-distance tandem sites.

  20. Short-pulse CO2 laser with longitudinal tandem discharge tube

    NASA Astrophysics Data System (ADS)

    Uno, K.; Akitsu, T.; Jitsuno, T.

    2014-10-01

    We developed a longitudinally excited CO2 laser with a tandem discharge tube. The tandem scheme was constituted of two 30-cm long discharge tubes connected with an intermediate electrode. Two parts, each consisting of a charged capacitance and a 30-cm long discharge tube, were electrically connected in parallel and switched by a spark gap. The tandem scheme produced a short laser pulse like that of a TEA-CO2 laser with a charging voltage of -24.8 kV, which was smaller than the -40.0 kV charging voltage of our previous CO2 laser. At a gas pressure of 3.8 kPa, the spike pulse width was 145 ns, the pulse tail length was 58.8 μs, the output energy was 52.0 mJ, and the spike pulse energy was 2.4 mJ. We also investigated the dependence of the laser pulse and the discharge voltage on gas pressure.

  1. Abundant contribution of short tandem repeats to gene expression variation in humans

    PubMed Central

    Gymrek, Melissa; Willems, Thomas; Guilmatre, Audrey; Zeng, Haoyang; Markus, Barak; Georgiev, Stoyan; Daly, Mark J.; Price, Alkes L.; Pritchard, Jonathan; Sharp, Andrew

    2016-01-01

    The contribution of repetitive elements to quantitative human traits is largely unknown. Here, we report a genome-wide survey of the contribution of Short Tandem Repeats (STRs), one of the most polymorphic and abundant repeat classes, to gene expression in humans. Our survey identified 2,060 significant expression STRs (eSTRs). These eSTRs were replicable in orthogonal populations and expression assays. We used variance partitioning to disentangle the contribution of eSTRs from linked SNPs and indels and found that eSTRs contribute 10%–15% of the cis-heritability mediated by all common variants. Further functional genomic analyses showed that eSTRs are enriched in conserved regions, co-localize with regulatory elements, and can modulate certain histone modifications. By analyzing known GWAS hits and searching for new associations in 1,685 deeply-phenotyped whole-genomes, we found that eSTRs are enriched in various clinically-relevant conditions. These results highlight the contribution of short tandem repeats to the genetic architecture of quantitative human traits. PMID:26642241

  2. Evaluation of 13 short tandem repeated loci for use in personal identification applications

    SciTech Connect

    Hammond, H.A.; Caskey, C.T. ); Jin, L.; Zhong, Y.; Chakraborty, R. )

    1994-07-01

    Personal identification by using DNA typing methodologies has been an issue in the popular and scientific press for several years. The authors present a PCR-based DNA-typing method using 13 unlinked short tandem repeat (STR) loci. Validation of the loci and methodology has been performed to meet standards set by the forensic community and the accrediting organization for parentage testing. Extensive statistical analysis has addressed the issues surrounding the presentation of [open quotes]match[close quotes] statistics. The authors have found STR loci to provide a rapid, sensitive, and reliable method of DNA typing for parentage testing, forensic identification, and medical diagnostics. Valid statistical analysis is generally simpler than similar analysis of RFLP-VNTR results and provides powerful statistical evidence of the low frequency of random multilocus genotype matching. 54 refs., 4 figs., 6 tabs.

  3. A study on ten short tandem repeat systems: African immigrant and Spanish population data.

    PubMed

    Gamero, J J; Romero, J L; Gonzalez, J L; Arufe, M I; Cuesta, M I; Corte-Real, F; Carvalho, M; Anjos, M J; Vieira, D N; Vide, M C

    2000-06-05

    This work presents the results obtained from a genetic-population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy-Weinberg equilibrium were detected.

  4. Short tandem repeat (STR) locus HUMD8S306 in a large population sample from Germany.

    PubMed

    Benecke, M; Knopf, M; Voll, W; Oesterreich, W; Jacobi, Y; Edelmann, J

    1998-10-01

    Applied DNA typing in medico-legal investigations, in criminalistic practice, and in paternity cases often relies on high inclusion and exclusion probabilities. For that reason, the short autosomal tandem repeat locus D8D306 was validated for forensic use and incorporated into a nonoverlapping multiplex reaction with HUMDHFRP2 and HUMCD4: The allele frequencies of D8S306 in four different regions of Germany (n = 1220 alleles) were determined for use in a population database; the allele distributions did not significantly deviate from each other. The hererozygosity of D8S306 is 83%, expected exclusion chance in stain cases is 96% (paternity cases: 69%), the lowest amount of successfully amplified DNA was 30 pg. The alleles are in Hardy-Weinberg equilibrium.

  5. Improved haplotype analysis of human myelin basic protein short tandem repeat loci.

    PubMed

    Watanabe, G; Umetsu, K; Yuasa, I; Suzuki, T

    2000-06-01

    We report an improved haplotype analysis of the human myelin basic protein gene (MBP) short tandem repeat (STR) polymorphism. The polymorphic G-->A transition and 2 conventional STR polymorphisms, MBPA and MBPB, were simultaneously determined by an amplified product length polymorphism technique. After the MBPC fragments containing MBPA and MBPB were amplified, the linkage of these 2 STR loci was determined by a second amplification, using polymerase chain reaction (PCR) technique, of the isolated MBPC fragments. The present haplotype analysis dispensed with family studies for the haplotyping of MBPA and MBPB. Polymorphisms of the MBP loci studied in German and Japanese populations showed a high genomic variation. Haplotype analysis of the MBP loci showed distinct differences between the German and the Japanese populations. Consequently, haplotype analysis of the MBP loci promises to be useful in forensic identification and paternity testing.

  6. Population genetic data of 15 tetrameric short tandem repeats (STRs) in Berbers from Morocco.

    PubMed

    Coudray, Clotilde; Guitard, Evelyne; Keyser-Tracqui, Christine; Melhaoui, Mohamed; Cherkaoui, Mohamed; Larrouy, Georges; Dugoujon, Jean-Michel

    2007-03-22

    The allele frequency distribution of 15 short tandem repeats (STR) loci contained in the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems), was determined in two Berber populations from Asni and Bouhria, in Central and Eastern Morocco, respectively. A total of 209 individuals were typed. No deviations from the Hardy-Weinberg equilibrium were observed for Asni at the 15 STRs loci whereas for the Bouhria samples, two loci (D5S818 and TH01) showed significant departures from Hardy-Weinberg expectations (after Bonferroni's correction). All loci are highly polymorphic and population differentiation tests showed that the Moroccan samples from Asni and Bouhria have significant differences in 4 out of 15 loci (D21S11, D7S820, D16S539 and TPOX). The aim of the study was to obtain accurate allele frequencies relevant for forensic applications. Comparative analyses between our population data and other population samples gathered from the literature are also presented.

  7. Transferability of short tandem repeat markers for two wild Canid species inhabiting the Brazilian Cerrado.

    PubMed

    Rodrigues, F M; Telles, M P C; Resende, L V; Soares, T N; Diniz-Filho, J A F; Jácomo, A T A; Silveira, L

    2006-12-13

    The maned wolf (Chrysocyon brachyurus) and the crab-eating fox (Cerdocyon thous) are two wild-canid species found in the Brazilian Cerrado. We tested cross-amplification and transferability of 29 short tandem repeat primers originally developed for cattle and domestic dogs and cats on 38 individuals of each of these two species, collected in the Emas National Park, which is the largest national park in the Cerrado region. Six of these primers were successfully transferred (CSSM-038, PEZ-05, PEZ-12, LOCO-13, LOCO-15, and PEZ-20); five of which were found to be polymorphic. Genetic parameter values (number of alleles per locus, observed and expected heterozygosities, and fixation indices) were within the expected range reported for canid populations worldwide.

  8. Population study and mutation analysis for 28 short tandem repeat loci in southwest Chinese Han population.

    PubMed

    Su, Qin; Jin, Bo; Luo, Haibo; Li, Yingbi; Wu, Jin; Yan, Jing; Hou, Yiping; Liang, Weibo; Zhang, Lin

    2016-11-01

    Short tandem repeat (STR) system is the most widely used genetic markers in modem forensic practice. Because of the relatively unstable molecular structure, STRs show a high mutation rate. In the current study, we report 169 mutation events of 13 CODIS and 15 non-CODIS STR loci that were found in 5569 cases of trios and duos paternity test. Our result indicated that locus-specific mutation rate varied among different populations, geometric means of the longest run of perfect repeats (LRPR) and heterozygosity. Along with previous published data, a forensic dataset for allele frequencies and locus-specific mutation rates of 13 CODIS and 15 non-CODIS STR loci from southwest Chinese Han population has been established. The mutation rate data have important implications in interpreting forensic individual identification and paternity testing.

  9. DNA Fingerprint Analysis of Three Short Tandem Repeat (STR) Loci for Biochemistry and Forensic Science Laboratory Courses

    ERIC Educational Resources Information Center

    McNamara-Schroeder, Kathleen; Olonan, Cheryl; Chu, Simon; Montoya, Maria C.; Alviri, Mahta; Ginty, Shannon; Love, John J.

    2006-01-01

    We have devised and implemented a DNA fingerprinting module for an upper division undergraduate laboratory based on the amplification and analysis of three of the 13 short tandem repeat loci that are required by the Federal Bureau of Investigation Combined DNA Index System (FBI CODIS) data base. Students first collect human epithelial (cheek)…

  10. DNA Fingerprint Analysis of Three Short Tandem Repeat (STR) Loci for Biochemistry and Forensic Science Laboratory Courses

    ERIC Educational Resources Information Center

    McNamara-Schroeder, Kathleen; Olonan, Cheryl; Chu, Simon; Montoya, Maria C.; Alviri, Mahta; Ginty, Shannon; Love, John J.

    2006-01-01

    We have devised and implemented a DNA fingerprinting module for an upper division undergraduate laboratory based on the amplification and analysis of three of the 13 short tandem repeat loci that are required by the Federal Bureau of Investigation Combined DNA Index System (FBI CODIS) data base. Students first collect human epithelial (cheek)…

  11. G-rich, a Drosophila selenoprotein, is a Golgi-resident type III membrane protein

    SciTech Connect

    Chen, Chang Lan; Shim, Myoung Sup; Chung, Jiyeol; Yoo, Hyun-Seung; Ha, Ji Min; Kim, Jin Young; Choi, Jinmi; Zang, Shu Liang; Hou, Xiao; Carlson, Bradley A.; Hatfield, Dolph L.; Lee, Byeong Jae . E-mail: imbglmg@plaza.snu.ac.kr

    2006-10-06

    G-rich is a Drosophila melanogaster selenoprotein, which is a homologue of human and mouse SelK. Subcellular localization analysis using GFP-tagged G-rich showed that G-rich was localized in the Golgi apparatus. The fusion protein was co-localized with the Golgi marker proteins but not with an endoplasmic reticulum (ER) marker protein in Drosophila SL2 cells. Bioinformatic analysis of G-rich suggests that this protein is either type II or type III transmembrane protein. To determine the type of transmembrane protein experimentally, GFP-G-rich in which GFP was tagged at the N-terminus of G-rich, or G-rich-GFP in which GFP was tagged at the C-terminus of G-rich, were expressed in SL2 cells. The tagged proteins were then digested with trypsin, and analyzed by Western blot analysis. The results showed that the C-terminus of the G-rich protein was exposed to the cytoplasm indicating it is a type III microsomal membrane protein. G-rich is First selenoprotein identified in the Golgi apparatus.

  12. Analysis of Y-chromosomal short tandem repeat (STR) polymorphism in an Iranian Sadat population.

    PubMed

    Rafiee, M R; Sokhansanj, A; Naghizadeh, M A; Farazmand, A

    2009-08-01

    The molecular genotyping of individuals and reconstruction of kinship through short and highly polymorphic DNA markers, so called short tandem repeats (STR), has become one of the important and efficient methods in anthropology studies and forensic science. Although many populations have been analyzed, no study has yet been carried out on Sadat populations who are putative descendents of Prophet Mohammad (peace be upon him). Polymorphisms of 6 Y-STR loci (DYS19, DYS385a/b, DYS389II, DYS390, DYS392, and DYS393) have been studied in an unrelated population of Sadat males. The aim of this study was to find possible similarities within Sadat males, resided in Iran. Among Sadat, DYS385b was proved to be the most polymorphic (GD = 0.8588), and DYS392 showed the lowest polymorphism (GD = 0.3527). In 50 samples, 45 different haplotypes were found, of which 39 haplotypes were unique. In the study, three samples had multi-allelic patterns. Haplotype diversity, in regard to these 7 markers was 0.9942.

  13. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

    PubMed

    Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

    2015-09-01

    The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome.

  14. Mass disasters: rapid molecular screening of human remains by means of short tandem repeats typing.

    PubMed

    Corach, D; Sala, A; Penacino, G; Sotelo, A

    1995-09-01

    Human remains identification represents a challenging situation and constitutes a difficult task associated with mass disasters. The only highly efficient means for individual and family group reconstruction is that based on DNA typing. On July 18, 1994 an explosion destroyed the A.M.I.A. (Argentine Israeli Association). Over 100 people died; however, the exact number of victims is still being investigated. Our Service received over 70 remains to be characterized by DNA typing in order to determine the number of victims and to try to reconstruct the family groups to which they belonged. DNA was extracted by a cetyltrimethylammonium bromide (CTAB) based protocol, a rapid molecular screening of all samples was carried out by multiplex STR amplifications including HUMTH01, HUMFABP, HUMHPRTB, HUMRENA4, HUMVWA, HUMFES/FPS and Y27H39LR. Samples with identical genotypes were HaeIII-digested. Southern blotted and probed with YNH-24 (D2S44). PH-30 (D4S139). LH-1 (D5S110) and MS-1 (D1S7) for variable number of tandem repeats (VNTR) evaluation. The minisatellite variant repeat (MVR) approach was used in those cases in which band or profile shift were detected in Southern blot assays. Kinship between victims and putative relatives was initially evaluated by comparison of short tandem repeat (STR) profiles and then confirmed by VNTR with the above probes. The high identification efficiency attained in this case is, in part, supported by a previous experience, the DNA-based molecular characterization of human remains caused by the explosion of the Israeli Embassy in Buenos Aires, March 1992.

  15. Developmental Validation of Short Tandem Repeat Reagent Kit for Forensic DNA Profiling of Canine Biological Materials

    PubMed Central

    Dayton, Melody; Koskinen, Mikko T; Tom, Bradley K; Mattila, Anna-Maria; Johnston, Eric; Halverson, Joy; Fantin, Dennis; DeNise, Sue; Budowle, Bruce; Smith, David Glenn; Kanthaswamy, Sree

    2009-01-01

    Aim To develop a reagent kit that enables multiplex polymerase chain reaction (PCR) amplification of 18 short tandem repeats (STR) and the canine sex-determining Zinc Finger marker. Methods Validation studies to determine the robustness and reliability in forensic DNA typing of this multiplex assay included sensitivity testing, reproducibility studies, intra- and inter-locus color balance studies, annealing temperature and cycle number studies, peak height ratio determination, characterization of artifacts such as stutter percentages and dye blobs, mixture analyses, species-specificity, case type samples analyses and population studies. Results The kit robustly amplified domesticated dog samples and consistently generated full 19-locus profiles from as little as 125 pg of dog DNA. In addition, wolf DNA samples could be analyzed with the kit. Conclusion The kit, which produces robust, reliable, and reproducible results, will be made available for the forensic research community after modifications based on this study’s evaluation to comply with the quality standards expected for forensic casework. PMID:19480022

  16. Multiplex short tandem repeat amplification of low template DNA samples with the addition of proofreading enzymes.

    PubMed

    Davis, Carey P; Chelland, Lynzee A; Pavlova, Victoria R; Illescas, María J; Brown, Kelly L; Cruz, Tracey Dawson

    2011-05-01

    With <100 pg of template DNA, routine short tandem repeat (STR) analysis often fails, resulting in no or partial profiles and increased stochastic effects. To overcome this, some have investigated preamplification methods that include the addition of proofreading enzymes to the PCR cocktail. This project sought to determine whether adding proofreading polymerases directly in the STR amplification mixture would improve the reaction when little template DNA is available. Platinum Taq High Fidelity and GeneAmp High Fidelity were tested in Profiler Plus™ STR reactions alone and in combination with AmpliTaq(®) Gold. All reactions included the additional step of a post-PCR purification step. With both pristine low template DNA and casework samples, the addition of these polymerases resulted in comparable or no improvement in the STR amplification signal. Further, stochastic effects and artifacts were observed equally across all enzyme conditions. Based on these studies, the addition of these proofreading enzymes to a multiplex STR amplification is not recommended for low template DNA work. © 2011 American Academy of Forensic Sciences.

  17. A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis.

    PubMed

    Reedy, Carmen R; Hagan, Kristin A; Marchiarullo, Daniel J; Dewald, Alison H; Barron, Annalise; Bienvenue, Joan M; Landers, James P

    2011-02-21

    Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples. Copyright © 2010 Elsevier B.V. All rights reserved.

  18. Global genetic variation at nine short tandem repeat loci and implications on forensic genetics.

    PubMed

    Sun, Guangyun; McGarvey, Stephen T; Bayoumi, Riad; Mulligan, Connie J; Barrantes, Ramiro; Raskin, Salmo; Zhong, Yixi; Akey, Joshua; Chakraborty, Ranajit; Deka, Ranjan

    2003-01-01

    We have studied genetic variation at nine autosomal short tandem repeat loci in 20 globally distributed human populations defined by geographic and ethnic origins, viz., African, Caucasian, Asian, Native American and Oceanic. The purpose of this study is to evaluate the utility and applicability of these nine loci in forensic analysis in worldwide populations. The levels of genetic variation measured by number of alleles, allele size variance and heterozygosity are high in all populations irrespective of their effective sizes. Single- as well as multi-locus genotype frequencies are in conformity with the assumptions of Hardy-Weinberg equilibrium. Further, alleles across the entire set of nine loci are mutually independent in all populations. Gene diversity analysis shows that pooling of population data by major geographic groupings does not introduce substructure effects beyond the levels recommended by the National Research Council, validating the establishment of population databases based on major geographic and ethnic groupings. A network tree based on genetic distances further supports this assertion, in which populations of common ancestry cluster together. With respect to the power of discrimination and exclusion probabilities, even the relatively reduced levels of genetic variation at these nine STR loci in smaller and isolated populations provide an exclusionary power over 99%. However, in paternity testing with unknown genotype of the mother, the power of exclusion could fall below 80% in some isolated populations, and in such cases use of additional loci supplementing the battery of the nine loci is recommended.

  19. Genome-wide identification of human- and primate-specific core promoter short tandem repeats.

    PubMed

    Bushehri, A; Barez, M R Mashhoudi; Mansouri, S K; Biglarian, A; Ohadi, M

    2016-08-01

    Recent reports of a link between human- and primate-specific genetic factors and human/primate-specific characteristics and diseases necessitate genome-wide identification of those factors. We have previously reported core promoter short tandem repeats (STRs) of extreme length (≥6-repeats) that have expanded exceptionally in primates vs. non-primates, and may have a function in adaptive evolution. In the study reported here, we extended our study to the human STRs of ≥3-repeats in the category of penta and hexaucleotide STRs, across the entire human protein coding gene core promoters, and analyzed their status in several superorders and orders of vertebrates, using the Ensembl database. The ConSite software was used to identify the transcription factor (TF) sets binding to those STRs. STR specificity was observed at different levels of human and non-human primate (NHP) evolution. 73% of the pentanucleotide STRs and 68% of the hexanucleotide STRs were found to be specific to human and NHPs. AP-2alpha, Sp1, and MZF were the predominantly selected TFs (90%) binding to the human-specific STRs. Furthermore, the number of TF sets binding to a given STR was found to be a selection factor for that STR. Our findings indicate that selected STRs, the cognate binding TFs, and the number of TF set binding to those STRs function as switch codes at different levels of human and NHP evolution and speciation.

  20. Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.

    PubMed

    Roewer, L; Krawczak, M; Willuweit, S; Nagy, M; Alves, C; Amorim, A; Anslinger, K; Augustin, C; Betz, A; Bosch, E; Cagliá, A; Carracedo, A; Corach, D; Dekairelle, A F; Dobosz, T; Dupuy, B M; Füredi, S; Gehrig, C; Gusmaõ, L; Henke, J; Henke, L; Hidding, M; Hohoff, C; Hoste, B; Jobling, M A; Kärgel, H J; de Knijff, P; Lessig, R; Liebeherr, E; Lorente, M; Martínez-Jarreta, B; Nievas, P; Nowak, M; Parson, W; Pascali, V L; Penacino, G; Ploski, R; Rolf, B; Sala, A; Schmidt, U; Schmitt, C; Schneider, P M; Szibor, R; Teifel-Greding, J; Kayser, M

    2001-05-15

    The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.

  1. Short tandem repeat (STR) variation in eight village populations of the island of Korcula (Croatia).

    PubMed

    Klarić, I M; Barać, L; Buković, D; Furać, I; Geber, G; Janićijević, B; Kubat, M; Pericić, M; Pupić, B V; Rudan, P

    2001-01-01

    The aim of this study was to analyse short tandem repeat (STR) variation using the data on nine loci (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, D7S820) in the populations from eight villages on the island of Korcula, Croatia, in order to analyse its genetic and population structure. The analysis of STR data in this study indicated an appreciable degree of genetic homogeneity among the studied village populations on the island, even though a so-called 'east-west dichotomy' and differentiation between the inhabitants of the most recent settlement and the remaining ones was indicated with respect to the loci CSF1PO and TPOX, respectively. The validity of STR markers in assessing genetic structure of small populations and especially in determining the relationships among geographically closely related but reproductively isolated groups remains to be further evaluated, especially in terms of a larger number of studied loci in order to possibly find specific markers useful for resolving genetic patterns of variability at regional levels.

  2. Allele Frequencies for 15 Short Tandem Repeat Loci in Representative Sample of Croatian Population

    PubMed Central

    Projić, Petar; Škaro, Vedrana; Šamija, Ivana; Pojskić, Naris; Durmić-Pašić, Adaleta; Kovačević, Lejla; Bakal, Narcisa; Primorac, Dragan; Marjanović, Damir

    2007-01-01

    Aim To study the distribution of allele frequencies of 15 short tandem repeat (STR) loci in a representative sample of the Croatian population. Methods A total of 195 unrelated Caucasian individuals born in Croatia, from 14 counties and the City of Zagreb, were sampled for the analysis. All the tested individuals were voluntary donors. Buccal swab was used as the DNA source. AmpFlSTR® Identifiler® was applied to simultaneously amplify 15 STR loci. Total reaction volume was 12.5 μL. The polymerase chain reaction (PCR) amplification was carried out in PE Gene Amp PCR System Thermal Cycler. Electrophoresis of the amplification products was preformed on an ABI PRISM 3130 Genetic Analyzer. After PCR amplification and separation by electrophoresis, raw data were compiled, analyzed, and numerical allele designations of the profiles were obtained. Deviation from Hardy-Weinberg equilibrium, observed and expected heterozygosity, power of discrimination, and power of exclusion were calculated. Bonferroni’s correction was used before each comparative analysis. Results We compared Croatian data with those obtained from geographically neighboring European populations. The significant difference (at P<0.01) in allele frequencies was recorded only between the Croatian and Slovenian populations for vWA locus. There was no significant deviation from Hardy-Weinberg equilibrium for all the observed loci. Conclusion Obtained population data concurred with the expected “STR data frame” for this part of Europe. PMID:17696301

  3. Validation of a Short Tandem Repeat Multiplex Typing System for Genetic Individualization of Domestic Cat Samples

    PubMed Central

    Coomber, Nikia; David, Victor A.; O’Brien, Stephen J.; Menotti-Raymond, Marilyn

    2007-01-01

    Aim To conduct developmental validation studies on a polymerase chain reaction (PCR) based short tandem repeat (STR) multiplex typing system, developed for the purpose of genetic individualization and parentage testing in domestic cat samples. Methods To evaluate reproducibility of the typing system, the multiplex was amplified using DNA extracted from hair, blood, and buccal samples obtained from the same individual (n = 13). Additional studies were performed to evaluate the system’s species’ specificity, using 26 North American mammalian species and two prokaryotes Sacchromyces and Escherichia coli, sensitivity, and ability to identify DNA mixtures. Patterns of Mendelian inheritance and mutation rates for the 11 loci were directly examined in a large multi-generation domestic cat pedigree (n = 263). Results Our studies confirm that the multiplex system was species-specific for feline DNA and amplified robustly with as little as 125 picograms of genomic template DNA, demonstrating good product balance. The multiplex generated all components of a two DNA mixture when the minor component was one tenth of the major component at a threshold of 50 relative fluorescence units. The multiplex was reproducible in multiple tissue types of the same individual. Mutation rates for the 11 STR were within the range of sex averaged rates observed for Combined DNA Index System (CODIS) loci. Conclusion The cat STR multiplex typing system is a robust and reliable tool for the use of forensic DNA analysis of domestic cat samples. PMID:17696310

  4. Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing.

    PubMed

    Darby, Brian J; Erickson, Shay F; Hervey, Samuel D; Ellis-Felege, Susan N

    2016-07-01

    High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data.

  5. An efficient clustering algorithm for partitioning Y-short tandem repeats data

    PubMed Central

    2012-01-01

    Background Y-Short Tandem Repeats (Y-STR) data consist of many similar and almost similar objects. This characteristic of Y-STR data causes two problems with partitioning: non-unique centroids and local minima problems. As a result, the existing partitioning algorithms produce poor clustering results. Results Our new algorithm, called k-Approximate Modal Haplotypes (k-AMH), obtains the highest clustering accuracy scores for five out of six datasets, and produces an equal performance for the remaining dataset. Furthermore, clustering accuracy scores of 100% are achieved for two of the datasets. The k-AMH algorithm records the highest mean accuracy score of 0.93 overall, compared to that of other algorithms: k-Population (0.91), k-Modes-RVF (0.81), New Fuzzy k-Modes (0.80), k-Modes (0.76), k-Modes-Hybrid 1 (0.76), k-Modes-Hybrid 2 (0.75), Fuzzy k-Modes (0.74), and k-Modes-UAVM (0.70). Conclusions The partitioning performance of the k-AMH algorithm for Y-STR data is superior to that of other algorithms, owing to its ability to solve the non-unique centroids and local minima problems. Our algorithm is also efficient in terms of time complexity, which is recorded as O(km(n-k)) and considered to be linear. PMID:23039132

  6. Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers.

    PubMed

    Asari, Masaru; Okuda, Katsuhiro; Hoshina, Chisato; Omura, Tomohiro; Tasaki, Yoshikazu; Shiono, Hiroshi; Matsubara, Kazuo; Shimizu, Keiko

    2016-02-01

    The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Genetic individualization of Cannabis sativa by a short tandem repeat multiplex system.

    PubMed

    Mendoza, Maria A; Mills, DeEtta K; Lata, Hemant; Chandra, Suman; ElSohly, Mahmoud A; Almirall, Jose R

    2009-01-01

    Cannabis sativa is the most frequently used of all illicit drugs in the USA. Cannabis has been used throughout history for its stems in the production of hemp fiber, seed for oil and food, and buds and leaves as a psychoactive drug. Short tandem repeats (STRs) were chosen as molecular markers owing to their distinct advantages over other genetic methods. STRs are codominant, can be standardized such that reproducibility between laboratories can be easily achieved, have a high discrimination power, and can be multiplexed. In this study, six STR markers previously described for C. sativa were multiplexed into one reaction. The multiplex reaction was able to individualize 98 cannabis samples (14 hemp and 84 marijuana, authenticated as originating from 33 of the 50 states of the USA) and detect 29 alleles averaging 4.8 alleles per loci. The data did not relate the samples from the same state to each other. This is the first study to report a single-reaction sixplex and apply it to the analysis of almost 100 cannabis samples of known geographic origin.

  8. Accurate size comparison of short tandem repeat alleles amplified by PCR.

    PubMed

    Smith, R N

    1995-01-01

    A strategy is presented for classifying complex short tandem repeat (STR) alleles by size. Such alleles can differ in length by only 1 bp. The HUMACTBP2 locus was used as a model. Dye-labeled, PCR-amplified alleles were analyzed on an automated DNA sequencer with laser-induced fluorescence detection and fragment-sizing software. Between-gel allele sizes calculated against an in-lane allelic ladder or viral DNA size standard were too imprecise to distinguish a 1-bp difference. However, the size difference between a sample allele and its matching ladder allele provided a reliable criterion for size classification. The mean size difference +/- 3 SDs was 0.5 bp, and so an individual result within this interval signified a match. Statistically, 99.7% of the results should lie within +/- 3 SDs with virtually no chance of encountering the 9-SD difference from the mean necessary to misclassify an allele by 1 bp. The method was valid for sample alleles sized against the allelic ladder and for both sample and ladder alleles sized against the viral DNA standard. A correction for the effect of different dye labels on mobility was included in the calculations.

  9. Seventeen Y-chromosomal short tandem repeat haplotypes in seven groups of population living in Taiwan.

    PubMed

    Hwa, Hsiao-Lin; Tseng, Li-Hui; Ko, Tsang-Ming; Chang, Yih-Yuan; Yin, Hsiang-Yi; Su, Yi-Ning; Lee, James Chun-I

    2010-07-01

    The analysis of Y-chromosome short tandem repeat (Y-STR) loci is a powerful tool in forensic casework. The aim of this study was to present the 17 Y-STR loci haplotype distributions of groups of population living in Taiwan and to demonstrate genetic distances between the groups as well as multidimensional scaling plot based on Y-STR genotype data. Five hundred and fifteen DNA samples from unrelated males of seven groups of population, including Taiwanese Han, two groups of indigenous Taiwanese of Taiwan Island, Tao, mainland Chinese, Filipinos, and a group of people with European, Near Eastern, or South Asian ancestry, were analyzed using a commercial kit that co-amplifies 17 Y-STRs. A total of 471 different haplotypes with 440 unique haplotypes were identified. The overall haplotype diversity was 0.9995 +/- 0.0002. High haplotype diversity was observed in six groups of population, except the Tao. These Y-STRs revealed a low discrimination capacity in the Tao population (36.84%), which should be considered in forensic practice. The multidimensional scaling plot of these seven groups of population constructed based on the genetic distances according to 17 Y-STR loci presented a clear patrilineal genetic substructure in the area. Partial Y-STRs profiling reduced the discrimination capacity in most groups of population and distorted the multidimensional scaling plot.

  10. Mutation and mutation rates at Y chromosome specific Short Tandem Repeat Polymorphisms (STRs): a reappraisal.

    PubMed

    Pinto, Nádia; Gusmão, Leonor; Amorim, António

    2014-03-01

    Mutation is a topic of intense research and raises important problems in forensics. Since the markers of choice in current forensic genetics analyses are microsatellites or Short Tandem Repeat Polymorphisms (STRs), mutation is sufficiently common to cause difficulties in evaluating DNA evidence in a significant proportion of cases but at the same time rare enough to turn the estimation of the corresponding probability of occurrence into a hard task. We address these issues using the simplest model of transmission: the Y chromosome specific STRs. Within this model, and under an explicit set of definitions and involved assumptions, we developed the theoretical framework required for the study of allelic transitions in gametogenesis, identifying the required parameters and associated probabilities and finally we discuss the estimation of these parameters and their application in forensics. We conclude that (i) for forensic casework the relevant parameter for incorporation in a likelihood ratio is biallelic specific (i.e. the mutation rate estimate corresponds to the probability of the specific allelic transition observed) and (ii) for these estimates as well as in order to provide data for testing mutation models the absolute frequency of mutated and non-mutated transmissions per allele, along with the description of the observed mutations should be reported.

  11. A simplified method for screening siblings for HLA identity using short tandem repeat (STR) polymorphisms.

    PubMed

    Schiller, Jennifer J; Hopp, Kathleen A; Pietz, Bradley C; Bick, David P; Lau, Eduardo C; Ellis, Thomas M

    2013-05-01

    Identifying an HLA-matched sibling donor for hematopoietic stem cell transplantation (HSCT) is time-consuming and expensive, and often limited by reimbursement caps imposed by insurance providers. To improve the effectiveness and efficiency of screening for HLA-matched siblings, we developed an assay for determining HLA identity using a panel of nine informative short tandem repeat (STR) loci located throughout the HLA complex. The STR panel was assessed for accuracy in identifying HLA-matched siblings in 88 family workups comprising a total of 132 related donor and recipient typing comparisons. All sibling pairs with identical STR alleles were also HLA identical. Of the 48 pairs mismatched at one or more STR alleles, all were genotypically HLA non-identical at one or more loci. The sensitivity and specificity of STR analysis for identifying HLA-matched siblings were 91% and 100%, respectively. Three false negatives occurred due to an STR mutation or possible HLA-DPB1/DQB1 recombination. Additionally, STR genotyping provided additional information allowing determination of the extent of HLA identity in families where HLA haplotype inheritance was ambiguous, due to extensive homozygosity or shared parental haplotypes. The HLA STR assay is a reliable and rapid test that can be used to inexpensively screen potential sibling donors for HLA identity.

  12. Cancer cell line identification by short tandem repeat profiling: power and limitations.

    PubMed

    Parson, Walther; Kirchebner, Romana; Mühlmann, Roswitha; Renner, Kathrin; Kofler, Anita; Schmidt, Stefan; Kofler, Reinhard

    2005-03-01

    Cancer cell lines are used worldwide in biological research, and data interpretation depends on unambiguous attribution of the respective cell line to its original source. Short-tandem-repeat (STR) profiling (DNA fingerprinting) is the method of choice for this purpose; however, the genetic stability of cell lines under various experimental conditions is not well defined. We tested the effect of long-term culture, subcloning, and generation of drug-resistant subclones on fingerprinting profiles in four widely used leukemia cell lines. The DNA fingerprinting profile remained unaltered in two of them (U937 and K562) throughout 12 months in culture, and the vast majority of subclones derived therefrom by limiting dilution after long-term culture revealed the same profile, indicating a high degree of stability and clonotypic homogeneity. In contrast, two other cell lines (CCRF-CEM and Jurkat) showed marked alterations in DNA fingerprinting profiles during long-term culture. Limiting dilution subcloning revealed extensive clonotypic heterogeneity with subclones differing in up to eight STR loci from the parental culture. Similar heterogeneity was observed in subclones generated by selection culture for drug resistance where DNA fingerprinting proved useful in identifying possible resistance mechanisms. Thus, common tissue culture procedures may dramatically affect the fingerprinting profile of certain cell lines and thus render definition of their origin difficult.

  13. A fully integrated microchip system for automated forensic short tandem repeat analysis.

    PubMed

    Han, Junping; Gan, Wupeng; Zhuang, Bin; Sun, Jing; Zhao, Lei; Ye, Jian; Liu, Yao; Li, Cai-Xia; Liu, Peng

    2017-05-30

    We have successfully developed an integrated microsystem that combines two plastic microchips for DNA extraction and PCR amplification with a glass capillary array electrophoresis chip together in a compact control and detection instrument for automated forensic short tandem repeat (STR) analysis. DNA extraction followed by an "in situ PCR" was conducted in a single reaction chamber of the microchip based on a filter paper-based extraction methodology. PCR products were then mixed with sizing standards by an injection electrode and injected into the electrophoresis chip for four-color confocal fluorescence detection. The entire STR analysis can be completed in about two hours without any human intervention. Since the 15-plex STR system has a more stringent requirement for PCR efficiency, we optimized the structure of the plastic DNA extraction and amplification chip, in which the reaction chamber was formed by sandwiching a hollow structure layer with two blank cover layers, to reduce the adsorption of PCR reagents to the surfaces. In addition, PCR additives, bovine serum albumin, poly(ethylene glycol), and more magnesium chloride were included into the on-chip multiplex STR system. The limit-of-detection study demonstrated that our microsystem was able to produce full 15-plex STR profiles from 3.75 ng standard K562 DNA. Buccal swab and whole blood samples were also successfully typed by our system, validating the feasibility of performing rapid DNA typing in a "sample-in-answer-out" manner for on-site forensic human identification.

  14. Optimization of DNA concentration to amplify short tandem repeats of human genomic DNA

    PubMed Central

    Gavazaj, Fahri Q.; Mikerezi, Ilia I.; Morina, Valon H.; Cakaj, Fatmir A.; Maloku, Ekrem B.; Gavazaj, Bahrije B.; Kastrati, Dhurata S.; Duriqi-Maloku, Besa A.

    2012-01-01

    Analysis of the length polymorphisms of short tandem repeats (STR) loci in the human genome has become a standard approach for comparative genotyping in many areas including disease research and diagnostics, parentage assessment, investigations of human diversity, and forensic science. The purpose of this study is to optimize the DNA concentration in ng/10μL for amplification of DNA markers. AmpFlSTR Identifiler Kit is used to amplify STR markers and capillary electrophoresis is used to analyze DNA profile of human the genome. Two sets of samples with following DNA concentration: 100 pg – 6 ng/25 μL were used for this study. There was no DNA profile detected in samples with concentrations 100 pg - 300 pg/25 μL (pictogram), while in some cases partial DNA profile was yielded. On the other hand samples with 0.4 ng – 4 ng/25 μL, yielded a full DNA profile. We were not able to obtain any profile using concentrations over 4 ng/25 μL. Improvements in detection limits/sensitivity at upper and lower DNA concentrations are of potential benefits to amplify STR of Human Genomic in order to obtain a full DNA profile. The optimal DNA concentrations which produced reliable and balanced peaks, no off scale peaks and full DNA profile for all loci were at range 0.4 ng – 3 ng/25 μL. PMID:23198938

  15. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing

    PubMed Central

    Warshauer, David H.; Churchill, Jennifer D.; Novroski, Nicole; King, Jonathan L.; Budowle, Bruce

    2015-01-01

    Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles. PMID:26391384

  16. Single-cell forensic short tandem repeat typing within microfluidic droplets.

    PubMed

    Geng, Tao; Novak, Richard; Mathies, Richard A

    2014-01-07

    A short tandem repeat (STR) typing method is developed for forensic identification of individual cells. In our strategy, monodisperse 1.5 nL agarose-in-oil droplets are produced with a high frequency using a microfluidic droplet generator. Statistically dilute single cells, along with primer-functionalized microbeads, are randomly compartmentalized in the droplets. Massively parallel single-cell droplet polymerase chain reaction (PCR) is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto the coencapsulated microbeads. These DNA-conjugated beads are subsequently harvested and reamplified under statistically dilute conditions for conventional capillary electrophoresis (CE) STR fragment size analysis. The 9-plex STR profiles of single cells from both pure and mixed populations of GM09947 and GM09948 human lymphoid cells show that all alleles are correctly called and allelic drop-in/drop-out is not observed. The cell mixture study exhibits a good linear relationship between the observed and input cell ratios in the range of 1:1 to 10:1. Additionally, the STR profile of GM09947 cells could be deduced even in the presence of a high concentration of cell-free contaminating 9948 genomic DNA. Our method will be valuable for the STR analysis of samples containing mixtures of cells/DNA from multiple contributors and for low-concentration samples.

  17. [Analysis of linkage disequilibrium and linkage for 12 short tandem repeat loci on chromosome X].

    PubMed

    Ye, Qiansu; Tang, Jianpin; Chen, Zucong; Li, Fagui; Yu, Xin; Wang, Ping; Lin, Hanguang; Shi, Meisen

    2014-12-01

    To analyze linkage disequilibrium of 12 short tandem repeat loci on chromosome X (X-STR) among an ethnic Han population from Guilin, Guangxi, and to study the genetic linkage and haplotype distributions of such loci in 2 linkage groups. 12 X-STR loci including DXS8378, DXS10159, DXS10162, DXS10164, DXS981, DXS6789, DXS7424, DXS101, DXS7133, GATA165B12, GATA31E08 and DXS7423 were genotyped using an AGCU X12 STR PCR Amplification kit. A total of 119 pedigrees were analyzed for linkage and linkage disequilibrium. Two mutations were found at DXS7424, and 1 mutation was found at DXS10164. A total of 93 haplotypes of DXS10159-DXS10162-DXS10164 were constructed for 261 unrelated males and females, in addition with 167 haplotypes of DXS6789-DXS7424-DXS101-DXS7133. The values of recombination fraction between DXS10159 and DXS10162, DXS10162 and DXS10164, DXS6789 and DXS7424, and DXS7424 and DXS101 were 0.0269, 0.0236, 0.0505 and 0.0438, respectively. Linkage disequilibrium of X-STR does not only depend on physical and genetic distances. There was incomplete linkage relationship between loci on DXS10159-DXS1016-DXS10164 and DXS6789-DXS7424-DXS101 linkage groups.

  18. Fetal sex identification in maternal plasma by means of short tandem repeats on chromosome x.

    PubMed

    Vecchione, Gennaro; Tomaiuolo, Michela; Sarno, Michelina; Colaizzo, Donatella; Petraroli, Rosella; Matteo, Maria; Greco, Pantaleo; Grandone, Elvira; Margaglione, Maurizio

    2008-08-01

    Analysis of fetal DNA in maternal plasma has recently been introduced as a new method for noninvasive prenatal diagnosis. In the majority of cases, the Y chromosome-specific sequences are commonly used as a fetus-specific marker with a high risk of false-negative cases. We attempted to develop a sensitive and reliable X chromosome short tandem repeat (STR) multiplex PCR amplification system that is suitable for the amplification of short-sized templates of free fetal DNA. Because of specific characteristics of fetal DNA in maternal plasma, cell-free fetal DNA is smaller than corresponding maternal DNA, and so we selected 10 X-STR loci in which the allele size was 250 bp. In addition, fetal sex was also investigated using the amelogenin gene in the same multiplex assay. Twenty-six women were enrolled in the study. Eight of 26 total fetuses analyzed were male and 18 were female. In the whole sample, X-STRs were informative with a mean of 4.84 +/- 1.43. A mean of 2.67 +/- 1.28 X-STR markers per sample (range 1-5) of paternally inherited fetal alleles were detected in pregnant women carrying a female fetus. In all cases, blind determination of fetal sex by means of the identification of amelogenin and X-STR markers was confirmed by fetal karyotyping. This study showed that this noninvasive technique is a reliable and accurate tool to investigate free fetal DNA in pregnancies within the first trimester and could be widely used in clinical research and diagnosis.

  19. How many single nucleotide polymorphisms (SNPs) are needed to replace short tandem repeats (STRs) in forensic applications?

    PubMed

    Lee, Hyo-Jung; Lee, Jae Won; Jeong, Su Jin; Park, Mira

    2017-02-27

    Short tandem repeats (STRs) are the most commonly used forms of genetic information in forensic identification. In recent times, advances in the information on single nucleotide polymorphisms (SNPs) have raised the possibility that these markers could replace the forensically established STRs. In this work, we conducted comparative simulation studies that allowed us to estimate the number of SNPs needed if these markers were used instead of STRs in criminal cases and paternity investigations.

  20. DNA fingerprint analysis of three short tandem repeat (STR) loci for biochemistry and forensic science laboratory courses.

    PubMed

    McNamara-Schroeder, Kathleen; Olonan, Cheryl; Chu, Simon; Montoya, Maria C; Alviri, Mahta; Ginty, Shannon; Love, John J

    2006-09-01

    We have devised and implemented a DNA fingerprinting module for an upper division undergraduate laboratory based on the amplification and analysis of three of the 13 short tandem repeat loci that are required by the Federal Bureau of Investigation Combined DNA Index System (FBI CODIS) data base. Students first collect human epithelial (cheek) cells using sterile buccal swabs and then utilize commercially available kits and materials to extract genomic DNA. This is followed by the PCR amplification of three specific short tandem repeat loci (i.e. CSF1PO, TPOX, THO1). Polyacrylamide gel electrophoresis is used to resolve the allelic bands associated with the three short tandem repeat loci, and the results are statistically analyzed in the context of human population genetics. In addition, DNA was collected from a family, and the children's allele sets were compared with those of the parents to help illustrate paternal and maternal relatedness. This module enables students to use the materials and methods employed by actual law enforcement agencies and therefore can be used for laboratory exercises in traditional biochemistry curricula as well as for the growing field of forensic science and education.

  1. Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues

    PubMed Central

    Barallon, Rita; Bauer, Steven R.; Butler, John; Capes-Davis, Amanda; Dirks, Wilhelm G.; Furtado, Manohar; Kline, Margaret C.; Kohara, Arihiro; Los, Georgyi V.; MacLeod, Roderick A. F.; Masters, John R. W.; Nardone, Mark; Nardone, Roland M.; Nims, Raymond W.; Price, Paul J.; Reid, Yvonne A.; Shewale, Jaiprakash; Sykes, Gregory; Steuer, Anton F.; Storts, Douglas R.; Thomson, Jim; Taraporewala, Zenobia; Alston-Roberts, Christine; Kerrigan, Liz

    2010-01-01

    Cell misidentification and cross-contamination have plagued biomedical research for as long as cells have been employed as research tools. Examples of misidentified cell lines continue to surface to this day. Efforts to eradicate the problem by raising awareness of the issue and by asking scientists voluntarily to take appropriate actions have not been successful. Unambiguous cell authentication is an essential step in the scientific process and should be an inherent consideration during peer review of papers submitted for publication or during review of grants submitted for funding. In order to facilitate proper identity testing, accurate, reliable, inexpensive, and standardized methods for authentication of cells and cell lines must be made available. To this end, an international team of scientists is, at this time, preparing a consensus standard on the authentication of human cells using short tandem repeat (STR) profiling. This standard, which will be submitted for review and approval as an American National Standard by the American National Standards Institute, will provide investigators guidance on the use of STR profiling for authenticating human cell lines. Such guidance will include methodological detail on the preparation of the DNA sample, the appropriate numbers and types of loci to be evaluated, and the interpretation and quality control of the results. Associated with the standard itself will be the establishment and maintenance of a public STR profile database under the auspices of the National Center for Biotechnology Information. The consensus standard is anticipated to be adopted by granting agencies and scientific journals as appropriate methodology for authenticating human cell lines, stem cells, and tissues. PMID:20614197

  2. Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea

    PubMed Central

    Moon, Seo Hyun; Jang, Yoon-Jeong

    2016-01-01

    Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)sib) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)sib values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)sib was about 3.35 × 10−5 for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes. PMID:26645337

  3. Development of a polymorphic short tandem repeat locus multiplex system for efficient human identification.

    PubMed

    Rodovalho, R G; Rodrigues, E L; Santos, G S; Cavalcanti, L M; Lima, P R; Rodovalho, A G; Vital, R G; Gigonzac, M A D; da Cruz, A D

    2017-04-05

    This study aimed to develop a short tandem repeat (STR) multiplex system, made up of 22 highly informative STR loci, for application in forensic genetics. The system comprised 21 polymorphic autosomal loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX, FGA, D2S441, D17S1301, D19S433, D18S853, D20S482, and D14S1434) and the amelogenin gene locus. Strategies were developed to overcome the challenges involved in creating a multiplex system. Based on the literature and available databases, the STR loci were selected with the aim to obtain discriminatory markers, and followed specific criteria for this purpose. Primers were projected using the Primer3 software, and AutoDimer was used to evaluate possible interactions between them. The 22 selected STR loci were validated individually and jointly, both to assess their sensitivity and to test the efficiency of the multiplex system. Statistical analyses were based on the genetic data of 450 unrelated individuals living in the State of Goiás, thus allowing the establishment of the parameters necessary to use this system. A total of 239 alleles were detected for the 22 loci in the set, allowing for a probability of identity of 4.23 x 10(-25) to be obtained. The combined power of discrimination was 0.999999999999999999999999 and the combined power of exclusion was 0.99999. Upon complete validation of the entire system, this multiplex assay was considered to be a powerful tool for application in human identification by DNA analysis.

  4. STRSeq: A catalog of sequence diversity at human identification Short Tandem Repeat loci.

    PubMed

    Gettings, Katherine Butler; Borsuk, Lisa A; Ballard, David; Bodner, Martin; Budowle, Bruce; Devesse, Laurence; King, Jonathan; Parson, Walther; Phillips, Christopher; Vallone, Peter M

    2017-09-01

    The STR Sequencing Project (STRSeq) was initiated to facilitate the description of sequence-based alleles at the Short Tandem Repeat (STR) loci targeted in human identification assays. This international collaborative effort, which has been endorsed by the ISFG DNA Commission, provides a framework for communication among laboratories. The initial data used to populate the project are the aggregate alleles observed in targeted sequencing studies across four laboratories: National Institute of Standards and Technology (N=1786), Kings College London (N=1043), University of North Texas Health Sciences Center (N=839), and University of Santiago de Compostela (N=944), for a total of 4612 individuals. STRSeq data are maintained as GenBank records at the U.S. National Center for Biotechnology Information (NCBI), which participates in a daily data exchange with the DNA DataBank of Japan (DDBJ) and the European Nucleotide Archive (ENA). Each GenBank record contains the observed sequence of a STR region, annotation ("bracketing") of the repeat region and flanking region polymorphisms, information regarding the sequencing assay and data quality, and backward compatible length-based allele designation. STRSeq GenBank records are organized within a BioProject at NCBI (https://www.ncbi.nlm.nih.gov/bioproject/380127), which is sub-divided into: commonly used autosomal STRs, alternate autosomal STRs, Y-chromosomal STRs, and X-chromosomal STRs. Each of these categories is further divided into locus-specific BioProjects. The BioProject hierarchy facilitates access to the GenBank records by browsing, BLAST searching, or ftp download. Future plans include user interface tools at strseq.nist.gov, a pathway for submission of additional allele records by laboratories performing population sample sequencing and interaction with the STRidER web portal for quality control (http://strider.online). Published by Elsevier B.V.

  5. Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification

    PubMed Central

    Nims, Raymond W.; Sykes, Greg; Cottrill, Karin; Ikonomi, Pranvera

    2010-01-01

    The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line’s species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification. PMID:20927602

  6. Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats

    PubMed Central

    Fungtammasan, Arkarachai; Tomaszkiewicz, Marta; Campos-Sánchez, Rebeca; Eckert, Kristin A.; DeGiorgio, Michael; Makova, Kateryna D.

    2016-01-01

    Transcript variation has important implications for organismal function in health and disease. Most transcriptome studies focus on assessing variation in gene expression levels and isoform representation. Variation at the level of transcript sequence is caused by RNA editing and transcription errors, and leads to nongenetically encoded transcript variants, or RNA–DNA differences (RDDs). Such variation has been understudied, in part because its detection is obscured by reverse transcription (RT) and sequencing errors. It has only been evaluated for intertranscript base substitution differences. Here, we investigated transcript sequence variation for short tandem repeats (STRs). We developed the first maximum-likelihood estimator (MLE) to infer RT error and RDD rates, taking next generation sequencing error rates into account. Using the MLE, we empirically evaluated RT error and RDD rates for STRs in a large-scale DNA and RNA replicated sequencing experiment conducted in a primate species. The RT error rates increased exponentially with STR length and were biased toward expansions. The RDD rates were approximately 1 order of magnitude lower than the RT error rates. The RT error rates estimated with the MLE from a primate data set were concordant with those estimated with an independent method, barcoded RNA sequencing, from a Caenorhabditis elegans data set. Our results have important implications for medical genomics, as STR allelic variation is associated with >40 diseases. STR nonallelic transcript variation can also contribute to disease phenotype. The MLE and empirical rates presented here can be used to evaluate the probability of disease-associated transcripts arising due to RDD. PMID:27413049

  7. lobSTR: A short tandem repeat profiler for personal genomes

    PubMed Central

    Gymrek, Melissa; Golan, David; Rosset, Saharon; Erlich, Yaniv

    2012-01-01

    Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat STR mapping as gapped alignment, which results in cumbersome processing times and a biased sampling of STR alleles. Here, we present lobSTR, a novel method for profiling STRs in personal genomes. lobSTR harnesses concepts from signal processing and statistical learning to avoid gapped alignment and to address the specific noise patterns in STR calling. The speed and reliability of lobSTR exceed the performance of current mainstream algorithms for STR profiling. We validated lobSTR's accuracy by measuring its consistency in calling STRs from whole-genome sequencing of two biological replicates from the same individual, by tracing Mendelian inheritance patterns in STR alleles in whole-genome sequencing of a HapMap trio, and by comparing lobSTR results to traditional molecular techniques. Encouraged by the speed and accuracy of lobSTR, we used the algorithm to conduct a comprehensive survey of STR variations in a deeply sequenced personal genome. We traced the mutation dynamics of close to 100,000 STR loci and observed more than 50,000 STR variations in a single genome. lobSTR's implementation is an end-to-end solution. The package accepts raw sequencing reads and provides the user with the genotyping results. It is written in C/C++, includes multi-threading capabilities, and is compatible with the BAM format. PMID:22522390

  8. Use of short tandem repeat analysis in unusual presentations of trophoblastic tumors and their mimics.

    PubMed

    Aranake-Chrisinger, John; Huettner, Phyllis C; Hagemann, Andrea R; Pfeifer, John D

    2016-06-01

    Gestational trophoblastic tumors can be difficult to distinguish from nongestational neoplasms. Somatic and germ cell tumors can mimic gestational choriocarcinoma, and epithelioid trophoblastic tumor (ETT) is known for its histologic, and sometimes clinical, resemblance to squamous cell carcinoma. Short tandem repeat (STR) analysis can separate gestational from nongestational neoplasms and can provide useful information about the type of causative conceptus. We present a series of cases which demonstrate the utility of STR analysis in the evaluation of gestational choriocarcinoma, epithelioid trophoblastic tumor, and their mimics. Samples from normal tissue and tumor were microdissected. DNA was extracted, and STR analysis was performed. Five cases were identified in which there was clinical and/or histologic concern for a gestational trophoblastic neoplasm. Case 1 is a choriocarcinoma presenting concurrently with a 16-week gestation. STR testing on the tumor, mother, and fetus showed that the tumor arose from a previous occult complete hydatidiform mole. Case 2 is an ETT presenting as multiple masses in bilateral kidneys, initially diagnosed as urothelial carcinoma. However, because of an elevated human chorionic gonadotropin, additional workup was performed which showed that the tumor was most likely an ETT. STR analysis showed that the tumor arose from a nonmolar pregnancy. Cases 3-5 illustrate somatic carcinomas mimicking gestational neoplasia. In those cases, STR confirmed a somatic origin. STR can be useful in distinguishing gestational from nongestational neoplasms, particularly in unusual settings. Also, STR analysis can add clinically useful information that is not available from clinical or histologic evaluation. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Evolutionary trend of exceptionally long human core promoter short tandem repeats.

    PubMed

    Ohadi, M; Mohammadparast, S; Darvish, H

    2012-10-01

    Short tandem repeats (STRs) are variable elements that play a significant role in genome evolution by creating and maintaining quantitative genetic variation. Because of their proximity to the +1 transcription start site (TSS) and polymorphic nature, core promoter STRs may be considered a novel source of variation across species. In a genome-scale analysis of the entire human protein-coding genes annotated in the GeneCards database (19,927), we analyze the prevalence and repeat numbers of different classes of core promoter STRs in the interval between -120 and +1 to the TSS. We also analyze the evolutionary trend of exceptionally long core promoter STRs of ≥6-repeats. 133 genes (~2%) had core promoter STRs of ≥6-repeats. In the majority of those genes, the STR motifs were found to be conserved across evolution. Di-nucleotide repeats had the highest representation in the human core promoter long STRs (72 genes). Tri- (52 genes), tetra-, penta-, and hexa-nucleotide STRs (9 genes) were also present in the descending prevalence. The majority of those genes (84 genes) revealed directional expansion of core promoter STRs from mouse to human. However, in a number of genes, the difference in average allele size across species was sufficiently small that there might be a constraint on the evolution of average allele size. Random drift of STRs from mouse to human was also observed in a minority of genes. Future work on the genes listed in the current study may further our knowledge into the potential importance of core promoter STRs in human evolution.

  10. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

    PubMed Central

    Ballantyne, Kaye N; Ralf, Arwin; Aboukhalid, Rachid; Achakzai, Niaz M; Anjos, Maria J; Ayub, Qasim; Balažic, Jože; Ballantyne, Jack; Ballard, David J; Berger, Burkhard; Bobillo, Cecilia; Bouabdellah, Mehdi; Burri, Helen; Capal, Tomas; Caratti, Stefano; Cárdenas, Jorge; Cartault, François; Carvalho, Elizeu F; Carvalho, Monica; Cheng, Baowen; Coble, Michael D; Comas, David; Corach, Daniel; D'Amato, Maria E; Davison, Sean; de Knijff, Peter; De Ungria, Maria Corazon A; Decorte, Ronny; Dobosz, Tadeusz; Dupuy, Berit M; Elmrghni, Samir; Gliwiński, Mateusz; Gomes, Sara C; Grol, Laurens; Haas, Cordula; Hanson, Erin; Henke, Jürgen; Henke, Lotte; Herrera-Rodríguez, Fabiola; Hill, Carolyn R; Holmlund, Gunilla; Honda, Katsuya; Immel, Uta-Dorothee; Inokuchi, Shota; Jobling, Mark A; Kaddura, Mahmoud; Kim, Jong S; Kim, Soon H; Kim, Wook; King, Turi E; Klausriegler, Eva; Kling, Daniel; Kovačević, Lejla; Kovatsi, Leda; Krajewski, Paweł; Kravchenko, Sergey; Larmuseau, Maarten H D; Lee, Eun Young; Lessig, Ruediger; Livshits, Ludmila A; Marjanović, Damir; Minarik, Marek; Mizuno, Natsuko; Moreira, Helena; Morling, Niels; Mukherjee, Meeta; Munier, Patrick; Nagaraju, Javaregowda; Neuhuber, Franz; Nie, Shengjie; Nilasitsataporn, Premlaphat; Nishi, Takeki; Oh, Hye H; Olofsson, Jill; Onofri, Valerio; Palo, Jukka U; Pamjav, Horolma; Parson, Walther; Petlach, Michal; Phillips, Christopher; Ploski, Rafal; Prasad, Samayamantri P R; Primorac, Dragan; Purnomo, Gludhug A; Purps, Josephine; Rangel-Villalobos, Hector; Rębała, Krzysztof; Rerkamnuaychoke, Budsaba; Gonzalez, Danel Rey; Robino, Carlo; Roewer, Lutz; Rosa, Alexandra; Sajantila, Antti; Sala, Andrea; Salvador, Jazelyn M; Sanz, Paula; Schmitt, Cornelia; Sharma, Anil K; Silva, Dayse A; Shin, Kyoung-Jin; Sijen, Titia; Sirker, Miriam; Siváková, Daniela; Škaro, Vedrana; Solano-Matamoros, Carlos; Souto, Luis; Stenzl, Vlastimil; Sudoyo, Herawati; Syndercombe-Court, Denise; Tagliabracci, Adriano; Taylor, Duncan; Tillmar, Andreas; Tsybovsky, Iosif S; Tyler-Smith, Chris; van der Gaag, Kristiaan J; Vanek, Daniel; Völgyi, Antónia; Ward, Denise; Willemse, Patricia; Yap, Eric PH; Yong, Rita YY; Pajnič, Irena Zupanič; Kayser, Manfred

    2014-01-01

    Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database. PMID:24917567

  11. Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea.

    PubMed

    Moon, Seo Hyun; Jang, Yoon-Jeong; Han, Myun Soo; Cho, Myung-Haing

    2016-09-30

    Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)sib) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)sib values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)sib was about 3.35 × 10(-)⁵ for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes.

  12. Core promoter short tandem repeats as evolutionary switch codes for primate speciation.

    PubMed

    Ohadi, Mina; Valipour, Elaheh; Ghadimi-Haddadan, Saeed; Namdar-Aligoodarzi, Pegah; Bagheri, Abouzar; Kowsari, Ali; Rezazadeh, Maryam; Darvish, Hossein; Kazeminasab, Somayeh

    2015-01-01

    Alteration in gene expression levels underlies many of the phenotypic differences across species. Because of their highly mutable nature, proximity to the +1 transcription start site (TSS), and the emerging evidence of functional impact on gene expression, core promoter short tandem repeats (STRs) may be considered an ideal source of variation across species. In a genome-scale analysis of the entire Homo sapiens protein-coding genes, we have previously identified core promoters with at least one STR of ≥ 6-repeats, with possible selective advantage in this species. In the current study, we performed reverse analysis of the entire Homo sapiens orthologous genes in mouse in the Ensembl database, in order to identify conserved STRs that have shrunk as an evolutionary advantage to humans. Two protocols were used to minimize ascertainment bias. Firstly, two species sharing a more recent ancestor with Homo sapiens (i.e. Pan troglodytes and Gorilla gorilla gorilla) were also included in the study. Secondly, four non-primate species encompassing the major orders across Mammals, including Scandentia, Laurasiatheria, Afrotheria, and Xenarthra were analyzed as out-groups. We introduce STR evolutionary events specifically identical in primates (i.e. Homo sapiens, Pan troglodytes, and Gorilla gorilla gorilla) vs. non-primate out-groups. The average frequency of the identically shared STR motifs across those primates ranged between 0.00005 and 0.06. The identified genes are involved in important evolutionary and developmental processes, such as normal craniofacial development (TFAP2B), regulation of cell shape (PALMD), learning and long-term memory (RGS14), nervous system development (GFRA2), embryonic limb morphogenesis (PBX2), and forebrain development (APAF1). We provide evidence of core promoter STRs as evolutionary switch codes for primate speciation, and the first instance of identity-by-descent for those motifs at the interspecies level. © 2014 Wiley Periodicals, Inc.

  13. Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.

    PubMed

    Fungtammasan, Arkarachai; Tomaszkiewicz, Marta; Campos-Sánchez, Rebeca; Eckert, Kristin A; DeGiorgio, Michael; Makova, Kateryna D

    2016-10-01

    Transcript variation has important implications for organismal function in health and disease. Most transcriptome studies focus on assessing variation in gene expression levels and isoform representation. Variation at the level of transcript sequence is caused by RNA editing and transcription errors, and leads to nongenetically encoded transcript variants, or RNA-DNA differences (RDDs). Such variation has been understudied, in part because its detection is obscured by reverse transcription (RT) and sequencing errors. It has only been evaluated for intertranscript base substitution differences. Here, we investigated transcript sequence variation for short tandem repeats (STRs). We developed the first maximum-likelihood estimator (MLE) to infer RT error and RDD rates, taking next generation sequencing error rates into account. Using the MLE, we empirically evaluated RT error and RDD rates for STRs in a large-scale DNA and RNA replicated sequencing experiment conducted in a primate species. The RT error rates increased exponentially with STR length and were biased toward expansions. The RDD rates were approximately 1 order of magnitude lower than the RT error rates. The RT error rates estimated with the MLE from a primate data set were concordant with those estimated with an independent method, barcoded RNA sequencing, from a Caenorhabditis elegans data set. Our results have important implications for medical genomics, as STR allelic variation is associated with >40 diseases. STR nonallelic transcript variation can also contribute to disease phenotype. The MLE and empirical rates presented here can be used to evaluate the probability of disease-associated transcripts arising due to RDD. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. Exceptionally long 5' UTR short tandem repeats specifically linked to primates.

    PubMed

    Namdar-Aligoodarzi, P; Mohammadparast, S; Zaker-Kandjani, B; Talebi Kakroodi, S; Jafari Vesiehsari, M; Ohadi, M

    2015-09-10

    We have previously reported genome-scale short tandem repeats (STRs) in the core promoter interval (i.e. -120 to +1 to the transcription start site) of protein-coding genes that have evolved identically in primates vs. non-primates. Those STRs may function as evolutionary switch codes for primate speciation. In the current study, we used the Ensembl database to analyze the 5' untranslated region (5' UTR) between +1 and +60 of the transcription start site of the entire human protein-coding genes annotated in the GeneCards database, in order to identify "exceptionally long" STRs (≥5-repeats), which may be of selective/adaptive advantage. The importance of this critical interval is its function as core promoter, and its effect on transcription and translation. In order to minimize ascertainment bias, we analyzed the evolutionary status of the human 5' UTR STRs of ≥5-repeats in several species encompassing six major orders and superorders across mammals, including primates, rodents, Scandentia, Laurasiatheria, Afrotheria, and Xenarthra. We introduce primate-specific STRs, and STRs which have expanded from mouse to primates. Identical co-occurrence of the identified STRs of rare average frequency between 0.006 and 0.0001 in primates supports a role for those motifs in processes that diverged primates from other mammals, such as neuronal differentiation (e.g. APOD and FGF4), and craniofacial development (e.g. FILIP1L). A number of the identified STRs of ≥5-repeats may be human-specific (e.g. ZMYM3 and DAZAP1). Future work is warranted to examine the importance of the listed genes in primate/human evolution, development, and disease.

  15. Genetic structure of the Azores Islands: a study using 15 autosomal short tandem repeat loci.

    PubMed

    Santos, Cristina; Alvarez, Luis; Aluja, Maria Pilar; Bruges-Armas, Jacome; Lima, Manuela

    2009-12-01

    The Azores archipelago (Portugal), located in the Atlantic Ocean, 1,500 km from the European mainland, is formed by nine islands of volcanic origin. The relative position of these islands allows the definition of three geographical groups: Eastern, Central and Western. Previous studies of the Azores using Short Tandem Repeats (STRs) have highlighted differences in the frequencies of several loci, when compared to Mainland Portugal or Madleira Island. Furthermore, linkage disequilibrium (LD), described for Azorean samples has been tentatively explained as reflecting the presence of genetic sub-structuring in the archipelago. To provide information concerning the genetic profile of the Azores Islands and to evaluate the presence of substructuring we have determined the allelic frequencies of 15 autosomal STR loci, using the AmpFlSTR Identifiler Kit, in representative samples from the Azorean Islands. Either considering the Azores as a whole, or analysing by island all the loci were in conformity with Hardy-Weinberg equilibrium. Average gene diversity ranged from 0.7669 in Corvo to 0.7972 in Terceira Island. Allelic independence between loci, tested for the global sample, detected significant LD (after correction for multiple tests) for pairs D21S11/D7S820 and D3S1358/D5S818. The exact test of population differentiation, combining the information of the 15 markers analysed, revealed significant differences between the three groups of islands, and between islands. Inter-island analysis reinforces the previous data that suggested the existence of sub-structuring in the Azores archipelago. Moreover, the data generated by this study can be used in a future forensic genetic database of the Azores after the appropriate enlacement of sample size by island, preventing, in that way, misinterpretations caused by population substructuring and small sample sizes.

  16. Fourteen non-CODIS autosomal short tandem repeat loci multiplex data from Taiwanese.

    PubMed

    Hwa, Hsiao-Lin; Chang, Yih-Yuan; Lee, James Chun-I; Yin, Hsiang-Yi; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

    2011-03-01

    Interest in the development of polymorphic short tandem repeat (STR) markers unlinked to the CODIS loci is growing among forensic practitioners. We developed a multiplex system in which14 autosomal STR (D3S1744, D4S2366, D8S1110, D12S1090, D13S765, D14S608, Penta E, D17S1294, D18S536, D18S1270, D20S470, D21S1437, Penta D, and D22S683) could be amplified in one single polymerase chain reaction. DNA samples from 572 unrelated Taiwanese Han subjects were analyzed using this 14 STR multiplex system. Thirty parent-child pairs of parentage testing cases with a combined paternity index (CPI) below 1,000 and 32 parent-child pairs with single-step mutations found in AmpFℓSTR Identifiler loci were also recruited for validation of the newly developed system. DNA sequencing was performed for novel STRs and novel alleles found in these subjects. The distributions of allelic frequencies for these autosomal STRs and sequence data, allele nomenclature for the STRs, and forensic parameters are presented. The discrimination power in our multiplex loci ranged from 0.6858 (D18S536) to 0.9168 (Penta E), with a combined discrimination power of 0.999999999. It provides additional power to distinguish the possible single-step mutations in parent-child pairs and improves the ability to prove parentage by increasing the CPI. The combined power of exclusion of these 14 loci in Taiwanese Han in this study was 0.9999995913. In conclusion, this 14-autosomal STRs multiplex system provides highly informative STR data and appears useful in forensic casework and parentage testing.

  17. [Conformational polymorphysm of G-rich fragments of DNA ALU-repeats. I. Potential noncanonical structures].

    PubMed

    Sekridova, A V; Varizhuk, A M; Tatarinova, O N; Severov, V V; Barinov, N A; Smirnov, I P; Lazarev, V N; Klinov, D V; Pozmogova, G E

    2016-07-01

    In this paper, we report results of systematic studies of conformational polymorphism of G-rich DNA fragments from Alu repeats. Alu retrotransposones are primate-specific short interspersed elements. Using the Alu sequence from the prooncogen bcl2 intron and the consensus AluSx sequence as representative examples, we determined characteristic Alu sites that are capable of adopting G-quadruplex (GQ) conformations (i.e., potential quadruplex sites - PQSAlu), and demonstrated by bioinformatics methods that those sites are Alu-specific in the human genome. Genomic frequencies of PQSAlu were assessed (~1/10000 b.p.). The sites were found to be characteristic of young (active) Alu families (Alu-Y). A recombinant DNA sequence bearing the Alu element from the human bcl2 gene (304 b.p.) and its PQS-mutant (Alu-PQS) were constructed. The formation of noncanonical structures in Alubcl2 dsDNA and the absence of such structures in the case of Alu-PQS were shown using DMS-footprinting and AFM microscopy. Expression vectors bearing wild-type and mutant Alu insertions in the promoter regions were obtained, and the effects of these insertions on the expression of the reporter gene in НЕК293 and HeLa cell lines were compared. Our findings on the spatial organization of Alu repeats may provide insight into the mechanisms of genomic rearrangements which underlie many oncological and neurodegenerative diseases.

  18. Least-square deconvolution: a framework for interpreting short tandem repeat mixtures.

    PubMed

    Wang, Tsewei; Xue, Ning; Birdwell, J Douglas

    2006-11-01

    Interpreting mixture short tandem repeat DNA data is often a laborious process, involving trying different genotype combinations mixed at assumed DNA mass proportions, and assessing whether the resultant is supported well by the relative peak-height information of the mixture sample. If a clear pattern of major-minor alleles is apparent, it is feasible to identify the major alleles of each locus and form a composite genotype profile for the major contributor. When alleles are shared between the two contributors, and/or heterozygous peak imbalance is present, it becomes complex and difficult to deduce the profile of the minor contributor. The manual trial and error procedures performed by an analyst in the attempt to resolve mixture samples have been formalized in the least-square deconvolution (LSD) framework reported here for two-person mixtures, with the allele peak height (or area) information as its only input. LSD operates on the peak-data information of each locus separately, independent of all other loci, and finds the best-fit DNA mass proportions and calculates error residual for each possible genotype combination. The LSD mathematical result for all loci is then to be reviewed by a DNA analyst, who will apply a set of heuristic interpretation guidelines in an attempt to form a composite DNA profile for each of the two contributors. Both simulated and forensic peak-height data were used to support this approach. A set of heuristic guidelines is to be used in forming a composite profile for each of the mixture contributors in analyzing the mathematical results of LSD. The heuristic rules involve the checking of consistency of the best-fit mass proportion ratios for the top-ranked genotype combination case among all four- and three-allele loci, and involve assessing the degree of fit of the top-ranked case relative to the fit of the second-ranked case. A different set of guidelines is used in reviewing and analyzing the LSD mathematical results for two

  19. An Ultra-High Discrimination Y Chromosome Short Tandem Repeat Multiplex DNA Typing System

    PubMed Central

    Hanson, Erin K.; Ballantyne, Jack

    2007-01-01

    In forensic casework, Y chromosome short tandem repeat markers (Y-STRs) are often used to identify a male donor DNA profile in the presence of excess quantities of female DNA, such as is found in many sexual assault investigations. Commercially available Y-STR multiplexes incorporating 12–17 loci are currently used in forensic casework (Promega's PowerPlex® Y and Applied Biosystems' AmpFlSTR® Yfiler®). Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants. Over 400 Y-STR loci have been identified on the Y chromosome. While these have the potential to increase the discrimination potential afforded by the commercially available kits, many have not been well characterized. In the present work, 91 loci were tested for their relative ability to increase the discrimination potential of the commonly used ‘core’ Y-STR loci. The result of this extensive evaluation was the development of an ultra high discrimination (UHD) multiplex DNA typing system that allows for the robust co-amplification of 14 non-core Y-STR loci. Population studies with a mixed African American and American Caucasian sample set (n = 572) indicated that the overall discriminatory potential of the UHD multiplex was superior to all commercial kits tested. The combined use of the UHD multiplex and the Applied Biosystems' AmpFlSTR® Yfiler® kit resulted in 100% discrimination of all individuals within the sample set, which presages its potential to maximally augment currently available forensic casework markers. It could also find applications in human evolutionary

  20. Short tandem repeat polymorphism linkage studies in a new family with X-linked mental retardation (MRX20)

    SciTech Connect

    Lazzarini, A.; Stenroos, E.S.; McKoy, V.

    1995-07-17

    A family with X-linked recessive mental retardation (XLMR) without other obvious manifestations (MRX20) was studied with 14 short tandem repeat polymorphism (STRP) markers. Two-point lod scores above 3 were obtained with DXS1003, DXYS1, DXS3, and DXS458. A multipoint lod score of 4.25 was obtained with peak at DXS1003. Recombination events identify a 55.6 cM interval between DXS1068 and DXS454, while a one unit support interval identifies 40 cM between MAOA and DXS458. 42 refs., 2 figs., 3 tabs.

  1. The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time

    PubMed Central

    Zhivotovsky, Lev A.; Underhill, Peter A.; Cinnioğlu, Cengiz; Kayser, Manfred; Morar, Bharti; Kivisild, Toomas; Scozzari, Rosaria; Cruciani, Fulvio; Destro-Bisol, Giovanni; Spedini, Gabriella; Chambers, Geoffrey K.; Herrera, Rene J.; Yong, Kiau Kiun; Gresham, David; Tournev, Ivailo; Feldman, Marcus W.; Kalaydjieva, Luba

    2004-01-01

    We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9×10-4 per 25 years, with a standard deviation across loci of 5.7×10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria. PMID:14691732

  2. Effects of Short-term Exposure to Inhalable Particulate Matter on DNA Methylation of Tandem Repeats

    PubMed Central

    Guo, Liqiong; Byun, Hyang-Min; Zhong, Jia; Motta, Valeria; Barupal, Jitendra; Zheng, Yinan; Dou, Chang; Zhang, Feiruo; McCracken, John P.; Diaz, Anaité; Marco, Sanchez-Guerra; Colicino, Silvia; Schwartz, Joel; Wang, Sheng; Hou, Lifang; Baccarelli, Andrea A.

    2015-01-01

    There is compelling evidence that particulate matter (PM) increases lung cancer risk by triggering systemic inflammation, and leukocyte DNA hypomethylation. However, previous investigations focused on repeated element sequences from LINE-1 and Alu families. Tandem repeats, which display a greater propensity to mutate, and are often hypomethylated in cancer patients, have never been investigated in individuals exposed to PM. We measured methylation of three tandem repeats (SATα, NBL2, D4Z4) by polymerase chain reaction–pyrosequencing on blood samples from truck drivers and office workers (60 per group) in Beijing, China. We used lightweight monitors to measure personal PM2.5 (PM with aerodynamic diameter ≤2.5 µm) and elemental carbon (EC, a tracer of PM from vehicular traffic). Ambient PM10 data were obtained from air quality measuring stations. Overall, an interquartile increase in personal PM2.5 and ambient PM10 levels was associated with a significant covariate-adjusted decrease in SATα methylation (−1.35% 5-methyl cytosine [5mC], P = 0.01; and −1.33%5mC; P = 0.01, respectively). Effects from personal PM2.5 and ambient PM10 on SATα methylation were stronger in truck drivers (−2.34%5mC, P = 0.02; −1.44%5mC, P = 0.06) than office workers (−0.95%5mC, P = 0.26; −1.25%5mC, P = 0.12, respectively). Ambient PM10 was negatively correlated with NBL2 methylation in truck drivers (−1.38%5mC, P = 0.03) but not in office workers (1.04%5mC, P = 0.13). Our result suggests that PM exposure is associated with hypomethylation of selected tandem repeats. Measuring tandem-repeat hypomethylation in easy-to-obtain blood specimens might identify individuals with biological effects and potential cancer risk from PM exposure. PMID:24436168

  3. The G-rich promoter and G-rich coding sequence of basic fibroblast growth factor are the targets of thalidomide in glioma.

    PubMed

    Mei, Szu-Chieh; Wu, Rong-Tsun

    2008-08-01

    Thalidomide is considered to be a potent antiangiogenic and immunomodulatory drug for cancer therapy. Earlier clinical studies have found that patients responding to this drug often had high plasma levels of basic fibroblast growth factor (bFGF). This cytokine is a proangiogenic factor overexpressed in many tumors and is also a regulator of limb development; hence, it might be a target of thalidomide. Using U-87 MG cell lines, we found that thalidomide, especially when encapsulated in a liposome, down-regulated the transcription and translation of the FGF-2 gene by interacting with G-rich regions present in the promoter and the internal ribosome entry site of its transcript at concentrations much lower than therapeutic serum concentrations. Thalidomide treatment also dramatically suppressed the anchorage-independent growth of U-87 MG and other glioma cells by over a thousand fold without affecting its anchorage-dependent growth, which may be accomplished by knocking down endogenous bFGF expression in these cells. Accordingly, the addition of recombinant bFGF partially restored the anchorage-independent growth of these cells. Our data suggest that by targeting the G-rich regions of bFGF, thalidomide (at 0.1 microg/mL) can reduce cellular bFGF levels and affect tumor anchorage-independent growth, the hallmark of tumorigenicity. Our results are promising for future clinical investigations using low doses of thalidomide.

  4. A simple Duplex-PCR to evaluate the DNA quality of anthropological and forensic samples prior short tandem repeat typing.

    PubMed

    von Wurmb-Schwark, Nicole; Schwark, Thorsten; Harbeck, Michaela; Oehmichen, Manfred

    2004-04-01

    Typing of DNA from ancient or otherwise highly degraded material, e.g. formalin fixed tissues, can be difficult, time consuming and costly. Very often, genetic typing is not possible at all. We present an inexpensive and easy to use Duplex-PCR that amplifies a 164 bp fragment specific for nuclear DNA together with a 260 bp mitochondrial DNA fragment and that can be employed as a pretest prior to short tandem repeat (STR) typing. All together, we analyzed DNA from 20 ancient bones, 20 formalin fixed tissues and 20 other forensic samples in different concentrations. Each sample that failed in the presented Duplex-amplification was also negative for STR typing, while samples that showed strong and clear signals in the Duplex-PCR led to reproducible genetic profiles using the multiplex kits AmpFLSTR Identifiler and Powerplex ES. The Duplex-PCR worked as a reliable indicator of DNA quality in the sample.

  5. Sequence-based definition of eight short tandem repeat loci located within the HLA-region in an Austrian population.

    PubMed

    Dauber, Eva-Maria; Wenda, Sabine; Schwartz-Jungl, Elisabeth Maria; Glock, Barbara; Mayr, Wolfgang R

    2015-01-01

    Sequenced allelic ladders are a prerequisite for reliable genotyping of short tandem repeat (STR) polymorphisms and consistent results across instrument platforms. For eight STR-loci located on the short arm of chromosome 6 (6p21.3), a sequenced based nomenclature was established according to international recommendations. Publicly available reference DNA samples were sequenced enabling interested laboratories to construct their own allelic ladders. Three tetrameric (D6S2691, D6S2678, DQIV), one trimeric (D6S2906) and four dimeric repeat loci (D6S2972, D6S2792, D6S2789, D6S273) were investigated. Apart from the very complex sequence structure at the DQIV locus, three loci showed a compound and four loci a simple repeat pattern. In the flanking regions of some loci additional single nucleotide and insertion/deletion polymorphisms occurred as well as sequence polymorphisms within the repeat region of alleles with the same length. In an Austrian Caucasoid population sample (n=293) between eight and 22 alleles were found. No significant deviation from Hardy-Weinberg expectations was observed, the power of discrimination ranged from 0.826 to 0.978. The loci cover the HLA-coding region from HLA-A to HLA-DQB1 and can be used for a better definition of HLA haplotypes for population and disease association studies, recombination point mapping, haematopoietic stem cell transplantation as well as for identity and relationship testing.

  6. Accurate mass determination of short-lived isotopes by a tandem Penning-trap mass spectrometer

    SciTech Connect

    Stolzenberg, H.; Becker, S.; Bollen, G.; Kern, F.; Kluge, H.; Otto, T.; Savard, G.; Schweikhard, L. ); Audi, G. ); Moore, R.B. ); The ISOLDE Collaboration

    1990-12-17

    A mass spectrometer consisting of two Penning traps has been set up for short-lived isotopes at the on-line mass separator ISOLDE at CERN. The ion beam is collected and cooled in the first trap. After delivery to the second trap, high-accuracy direct mass measurements are made by determining the cyclotron frequency of the stored ions. Measurements have been performed for {sup 118}Cs--{sup 137}Cs. A resolving power of over 10{sup 6} and an accuracy of 1.4{times}10{sup {minus}7} have been achieved, corresponding to about 20 keV.

  7. A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci.

    PubMed

    Gill, Peter; Curran, James; Elliot, Keith

    2005-01-01

    The use of expert systems to interpret short tandem repeat DNA profiles in forensic, medical and ancient DNA applications is becoming increasingly prevalent as high-throughput analytical systems generate large amounts of data that are time-consuming to process. With special reference to low copy number (LCN) applications, we use a graphical model to simulate stochastic variation associated with the entire DNA process starting with extraction of sample, followed by the processing associated with the preparation of a PCR reaction mixture and PCR itself. Each part of the process is modelled with input efficiency parameters. Then, the key output parameters that define the characteristics of a DNA profile are derived, namely heterozygote balance (Hb) and the probability of allelic drop-out p(D). The model can be used to estimate the unknown efficiency parameters, such as pi(extraction). 'What-if' scenarios can be used to improve and optimize the entire process, e.g. by increasing the aliquot forwarded to PCR, the improvement expected to a given DNA profile can be reliably predicted. We demonstrate that Hb and drop-out are mainly a function of stochastic effect of pre-PCR molecular selection. Whole genome amplification is unlikely to give any benefit over conventional PCR for LCN.

  8. Fifteen non-CODIS autosomal short tandem repeat loci multiplex data from nine population groups living in Taiwan.

    PubMed

    Hwa, Hsiao-Lin; Chang, Yih-Yuan; Lee, James Chun-I; Lin, Chun-Yen; Yin, Hsiang-Yi; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

    2012-07-01

    The analysis of autosomal short tandem repeat (STR) loci is a powerful tool in forensic genetics. We developed a multiplex system in which 15 non-Combined DNA Index System autosomal STRs (D3S1744, D4S2366, D8S1110, D10S2325, D12S1090, D13S765, D14S608, Penta E, D17S1294, D18S536, D18S1270, D20S470, D21S1437, Penta D, and D22S683) could be amplified in one single polymerase chain reaction. DNA samples from 1,098 unrelated subjects of nine population groups living in Taiwan, including Taiwanese Han, indigenous Taiwanese of Taiwan Island, Tao, mainland Chinese, Filipinos, Thais, Vietnamese, Indonesians, and Caucasians, were collected and analyzed using this system. The distributions of the allelic frequencies and the forensic parameters of each population group were presented. The combined discrimination power and the combined power of exclusion were high in all population groups tested in this study. A multidimensional scaling plot of these nine population groups based on the Reynolds' genetic distances calculated from 15 autosomal STRs was constructed, and the genetic substructure in this area was presented. In conclusion, this 15 autosomal STR multiplex system provides highly informative STR data and appears useful in forensic casework and parentage testing in different populations.

  9. The development and application of a multiplex short tandem repeat (STR) system for identifying subspecies, individuals and sex in tigers.

    PubMed

    Zou, Zheng-Ting; Uphyrkina, Olga V; Fomenko, Pavel; Luo, Shu-Jin

    2015-07-01

    Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system "tigrisPlex" to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA. With DNA samples used for between-run calibration, the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles, hence making it possible to identify subspecies via bi-parentally inherited markers. We applied "tigrisPlex" to 12 confiscated specimens from Russia and identified 6 individuals (3 females and 3 males), each represented by duplicated samples and all designated as Amur tigers (Panthera tigris altaica) with high confidence. This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products, fulfilling various conservation needs for identifying the origins of tiger samples. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

  10. Highly Effective DNA Extraction Method for Nuclear Short Tandem Repeat Testing of Skeletal Remains from Mass Graves

    PubMed Central

    Davoren, Jon; Vanek, Daniel; Konjhodzić, Rijad; Crews, John; Huffine, Edwin; Parsons, Thomas J.

    2007-01-01

    Aim To quantitatively compare a silica extraction method with a commonly used phenol/chloroform extraction method for DNA analysis of specimens exhumed from mass graves. Methods DNA was extracted from twenty randomly chosen femur samples, using the International Commission on Missing Persons (ICMP) silica method, based on Qiagen Blood Maxi Kit, and compared with the DNA extracted by the standard phenol/chloroform-based method. The efficacy of extraction methods was compared by real time polymerase chain reaction (PCR) to measure DNA quantity and the presence of inhibitors and by amplification with the PowerPlex 16 (PP16) multiplex nuclear short tandem repeat (STR) kit. Results DNA quantification results showed that the silica-based method extracted on average 1.94 ng of DNA per gram of bone (range 0.25-9.58 ng/g), compared with only 0.68 ng/g by the organic method extracted (range 0.0016-4.4880 ng/g). Inhibition tests showed that there were on average significantly lower levels of PCR inhibitors in DNA isolated by the organic method. When amplified with PP16, all samples extracted by silica-based method produced 16 full loci profiles, while only 75% of the DNA extracts obtained by organic technique amplified 16 loci profiles. Conclusions The silica-based extraction method showed better results in nuclear STR typing from degraded bone samples than a commonly used phenol/chloroform method. PMID:17696302

  11. A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci

    PubMed Central

    Gill, Peter; Curran, James; Elliot, Keith

    2005-01-01

    The use of expert systems to interpret short tandem repeat DNA profiles in forensic, medical and ancient DNA applications is becoming increasingly prevalent as high-throughput analytical systems generate large amounts of data that are time-consuming to process. With special reference to low copy number (LCN) applications, we use a graphical model to simulate stochastic variation associated with the entire DNA process starting with extraction of sample, followed by the processing associated with the preparation of a PCR reaction mixture and PCR itself. Each part of the process is modelled with input efficiency parameters. Then, the key output parameters that define the characteristics of a DNA profile are derived, namely heterozygote balance (Hb) and the probability of allelic drop-out p(D). The model can be used to estimate the unknown efficiency parameters, such as πextraction. ‘What-if’ scenarios can be used to improve and optimize the entire process, e.g. by increasing the aliquot forwarded to PCR, the improvement expected to a given DNA profile can be reliably predicted. We demonstrate that Hb and drop-out are mainly a function of stochastic effect of pre-PCR molecular selection. Whole genome amplification is unlikely to give any benefit over conventional PCR for LCN. PMID:15681615

  12. Detection of aneuploidies in spontaneous abortions by quantitative fluorescent PCR with short tandem repeat markers: a retrospective study.

    PubMed

    Coelho, F F; Marques, F K; Gonçalves, M S; Almeida, V C O; Mateo, E C C; Ferreira, A C S

    2016-09-23

    Approximately 10-15% of all pregnancies end in spontaneous abortions. Many factors can lead to embryonic loss; however, it has been well established that over 50% of all miscarriages result from chromosomal abnormalities, primarily aneuploidies (>96%). Identifying the cause of miscarriage can significantly reduce the psychological stress in women, and enable better genetic counseling for a future pregnancy. Quantitative fluorescent polymerase chain reaction (QF-PCR) has been previously used in the study of chromosomal abnormalities. In this retrospective study, the frequency of aneuploidy in samples of 130 miscarriages undergone by patients (age average: 34.1 ± 4.6 years) at our institution was determined by QF-PCR using short tandem repeat markers. The gender of the miscarriage cases was determined by amplifying the amelogenin locus (70 males and 60 females). Seventy-one of these cases (54.6%) presented aneuploidies such as trisomy, monosomy, triploidy, and double trisomy. Trisomy 22 was the most common aneuploidy (present in 14 cases), followed by trisomy 15, trisomy 16, and monosomy X. We also observed monosomy at chromosomes X and 21 and a case with multiple aneuploidies at chromosomes 16 and 22. The most common aneuploidies associated with miscarriages were detected by QF-PCR; therefore, we concluded that QF-PCR is a rapid and reliable method for the detection of aneuploidy, and can be used as an accessory to the widely used karyotype analysis.

  13. Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization.

    PubMed

    Diegoli, Toni Marie; Rohde, Heinrich; Borowski, Stefan; Krawczak, Michael; Coble, Michael D; Nothnagel, Michael

    2016-11-01

    Typing of X chromosomal short tandem repeat (X STR) markers has become a standard element of human forensic genetic analysis. Joint consideration of many X STR markers at a time increases their discriminatory power but, owing to physical linkage, requires inter-marker recombination rates to be accurately known. We estimated the recombination rates between 15 well established X STR markers using genotype data from 158 families (1041 individuals) and following a previously proposed likelihood-based approach that allows for single-step mutations. To meet the computational requirements of this family-based type of analysis, we modified a previous implementation so as to allow multi-core parallelization on a high-performance computing system. While we obtained recombination rate estimates larger than zero for all but one pair of adjacent markers within the four previously proposed linkage groups, none of the three X STR pairs defining the junctions of these groups yielded a recombination rate estimate of 0.50. Corroborating previous studies, our results therefore argue against a simple model of independent X chromosomal linkage groups. Moreover, the refined recombination fraction estimates obtained in our study will facilitate the appropriate joint consideration of all 15 investigated markers in forensic analysis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. Application of Short Tandem Repeat markers in diagnosis of chromosomal aneuploidies and forensic DNA investigation in Pakistan.

    PubMed

    Chishti, Hafsah Muhammad; Ansar, Muhammad; Ajmal, Muhammad; Hameed, Abdul

    2014-09-15

    Short Tandem Repeat (STR) genetic markers hold great potential in forensic investigations, molecular diagnostics and molecular genetics research. AmpFlSTR® Identifiler™ PCR amplification kit is a multiplex system for co-amplification of 15 STR markers used worldwide in forensic investigations. This study attempts to assess forensic validity of these STRs in Pakistani population and to investigate its applicability in quick and simultaneous diagnosis and tracing parental source of common chromosomal aneuploidies. Samples from 554 healthy Pakistani individuals from 5 different ethnicities were analyzed for forensic parameters using Identifiler STRs and 74 patients' samples with different aneuploidies were evaluated for diagnostic strengths of these markers. All STRs hold sufficient forensic applicability in Pakistani population with paternity index between 1.5 and 3.5, polymorphic information content from 0.63 to 0.87 and discrimination power ≥0.9 (except TPOX locus). Variation from Hardy-Weinberg equilibrium was observed at some loci reflecting selective breeding and intermarriages trend in Pakistan. Among aneuploidic samples, all trisomies were precisely detectable while aneuploidies involving sex chromosomes or missing chromosomes were not clearly detectable using Identifiler STRs. Parental origin of aneuploidy was traceable in 92.54% patients. The studied STR markers are valuable tools for forensic application in Pakistan and utilizable for quick and simultaneous identification of some common trisomic conditions. Adding more sex chromosome specific STR markers can immensely increase the diagnostic and forensic potential of this system. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. [Genetic polymorphisms of 9 non-combined of DNA index system short tandem repeat loci in Guangdong Han population].

    PubMed

    Zhang, Jin-xiang; Xue, Tian-yu; Li, Hai-xia; Sun, Hong-yu; Cheng, Jian-ding

    2009-10-01

    To investigate the genetic polymorphisms and their forensic application of 9 non-combined of DNA index system (CODIS) short tandem repeat(STR) loci in Guangdong Han population. DNA samples from 500 unrelated individuals were extracted and amplified with fluorescence labeled multiplex PCR system. PCR products were separated and genotyped with capillary electrophoresis. One hundred and fifteen alleles and 160 genotypes were observed in the 9 STR loci, respectively. The heterozygosity was 0.824-0.884, the discrimination power (DP) was 0.925-0.969 and the polymorphism information content (PIC) was 0.77-0.86, respectively. The distribution met the Hardy-Weinberg equilibrium (P > 0.05). The total discrimination power was 1.00 x 10(-13), the combined probability of exclusion for trio-paternity testing was 0.999989488. The combined probability of exclusion for duo-paternity testing was 0.873436. The 9 STR loci are powerful and reliable for personal identification and paternity testing. They can be used as supplementary loci in fatherless (motherless) testing or cases with mutation events.

  16. Short tandem repeat polymorphism in the flanking region of the human phosphoglycerate kinase gene in a Japanese population.

    PubMed

    Tie, Jian; Serizawa, Yuka; Oshida, Shigemi; Usami, Ron; Yoshida, Yasuhiko

    2006-04-01

    The human phosphoglycerate kinase (PGK1) gene is located within Xqll-Xql3 and is closely linked to the androgen receptor gene within a region implicated in a number of X-chromosome-linked urologic disorders. A polymorphism of a TATC short tandem repeat (STR) is present downstream from the PGK1 3' nuclease-sensitive site. We present the PGK1 flanking STR sequence and population genetic data for 190 Japanese males and 83 Japanese females. Ten STR alleles and 29 genotypes were identified in the population. Five alleles--*10, *11, *12, *13, and *14--were common in the Japanese with frequencies greater than 10%. No significant deviations from Hardy-Weinberg equilibrium were established. The power of discrimination was 0.993 for females and 0.819 for males; heterozygosity was 0.759 for females; and the polymorphic information content was 0.936. These data indicate that this STR locus shows a high degree of polymorphism in this Japanese population and may prove to be a useful genetic marker in forensic medicine, in determining the clonality of neoplasms, and potentially in studying predisposition to prostate cancer and other urologic diseases.

  17. VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations

    PubMed Central

    Trimarsanto, Hidayat; Benavente, Ernest D.; Noviyanti, Rintis; Utami, Retno Ayu Setya; Trianty, Leily; Pava, Zuleima; Getachew, Sisay; Kim, Jung-Yeon; Goo, Youn-Kyoung; Wangchuck, Sonam; Liu, Yaobao; Gao, Qi; Dowd, Simone; Cheng, Qin; Clark, Taane G.; Price, Ric N.

    2017-01-01

    Background The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics, through the application of genotyping and population genetics analyses. This paper describes VivaxGEN (http://vivaxgen.menzies.edu.au), a web-based platform that has been developed to support P. vivax short tandem repeat data sharing and comparative analyses. Results The VivaxGEN platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools. The query system of the platform enables users to filter, select and differentiate samples and alleles based on their specified criteria. Key population genetic analyses are supported including measures of population differentiation (FST), expected heterozygosity (HE), linkage disequilibrium (IAS), neighbor-joining analysis and Principal Coordinate Analysis. Datasets can also be formatted and exported for application in commonly used population genetic software including GENEPOP, Arlequin and STRUCTURE. To date, data from 10 countries, including 5 publicly available data sets have been shared with VivaxGEN. Conclusions VivaxGEN is well placed to facilitate regional overviews of P. vivax transmission dynamics in different endemic settings and capable to be adapted for similar genetic studies of P. falciparum and other organisms. PMID:28362818

  18. Intra- and inter-population diversity at short tandem repeat loci in diverse populations of the world.

    PubMed

    Deka, R; Shriver, M D; Yu, L M; Ferrell, R E; Chakraborty, R

    1995-09-01

    To study the level of intra- and inter-population variation at hypervariable DNA loci, we have characterized 15 human populations of diverse ethnic and geographic origins at six short tandem repeat loci by using the polymerase chain reaction. Even though the spectrum of allelic variation is quite broad and there are substantial differences in allele frequency distributions among populations, in general, population within a major racial group show a greater degree of similarity. This observation is reflected in the analysis of gene diversity. When the total diversity is apportioned, the maximum variation becomes attributable to inter-individual differences within a population; of the variation that is attributed to differences between populations within a racial group and differences between racial groups, namely, African, Caucasian, and Mongoloid, than the American Indians and the Pacific Islanders. As expected, a reciprocal relationship between gene diversity and FST levels is observed. Higher values of FST in the American Indian and the Pacific Islanders may reflect smaller population size and a higher level of isolation. An analysis of genetic distance encompassing the populations belonging to the three major racial groups recognizes three distinct clusters - all the populations of African affiliation cluster together, as do the Caucasian affiliated and the Mongoloid groups, in two distinct clusters. Interestingly, three broadly classified cosmopolitan US populations, namely, US White, US Black and US Asian, cluster with their ancestrally related populations. This study dispels some of the concerns regarding the applicability of DNA typing data for forensic use.

  19. A valveless microfluidic device for integrated solid phase extraction and polymerase chain reaction for short tandem repeat (STR) analysis.

    PubMed

    Hagan, Kristin A; Reedy, Carmen R; Bienvenue, Joan M; Dewald, Alison H; Landers, James P

    2011-05-07

    A valveless microdevice has been developed for the integration of solid phase extraction (SPE) and polymerase chain reaction (PCR) on a single chip for the short tandem repeat (STR) analysis of DNA from a biological sample. The device consists of two domains--a SPE domain filled with silica beads as a solid phase and a PCR domain with an ~500 nL reaction chamber. DNA from buccal swabs was purified and amplified using the integrated device and a full STR profile (16 loci) resulted. The 16 loci Identifiler® multiplex amplification was performed using a non-contact infrared (IR)-mediated PCR system built in-house, after syringe-driven SPE, providing an ~80-fold and 2.2-fold reduction in sample and reagent volumes consumed, respectively, as well as an ~5-fold reduction in the overall analysis time in comparison to conventional analysis. Results indicate that the SPE-PCR system can be used for many applications requiring genetic analysis, and the future addition of microchip electrophoresis (ME) to the system would allow for the complete processing of biological samples for forensic STR analysis on a single microdevice.

  20. Towards Development of Clustering Applications for Large-Scale Comparative Genotyping and Kinship Analysis Using Y-Short Tandem Repeats

    PubMed Central

    Sapawi, Azizian Mohd; Salleh, Mohd Zaki

    2015-01-01

    Abstract Y-chromosome short tandem repeats (Y-STRs) are genetic markers with practical applications in human identification. However, where mass identification is required (e.g., in the aftermath of disasters with significant fatalities), the efficiency of the process could be improved with new statistical approaches. Clustering applications are relatively new tools for large-scale comparative genotyping, and the k-Approximate Modal Haplotype (k-AMH), an efficient algorithm for clustering large-scale Y-STR data, represents a promising method for developing these tools. In this study we improved the k-AMH and produced three new algorithms: the Nk-AMH I (including a new initial cluster center selection), the Nk-AMH II (including a new dominant weighting value), and the Nk-AMH III (combining I and II). The Nk-AMH III was the superior algorithm, with mean clustering accuracy that increased in four out of six datasets and remained at 100% in the other two. Additionally, the Nk-AMH III achieved a 2% higher overall mean clustering accuracy score than the k-AMH, as well as optimal accuracy for all datasets (0.84–1.00). With inclusion of the two new methods, the Nk-AMH III produced an optimal solution for clustering Y-STR data; thus, the algorithm has potential for further development towards fully automatic clustering of any large-scale genotypic data. PMID:25945508

  1. VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations.

    PubMed

    Trimarsanto, Hidayat; Benavente, Ernest D; Noviyanti, Rintis; Utami, Retno Ayu Setya; Trianty, Leily; Pava, Zuleima; Getachew, Sisay; Kim, Jung-Yeon; Goo, Youn-Kyoung; Wangchuck, Sonam; Liu, Yaobao; Gao, Qi; Dowd, Simone; Cheng, Qin; Clark, Taane G; Price, Ric N; Auburn, Sarah

    2017-03-01

    The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics, through the application of genotyping and population genetics analyses. This paper describes VivaxGEN (http://vivaxgen.menzies.edu.au), a web-based platform that has been developed to support P. vivax short tandem repeat data sharing and comparative analyses. The VivaxGEN platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools. The query system of the platform enables users to filter, select and differentiate samples and alleles based on their specified criteria. Key population genetic analyses are supported including measures of population differentiation (FST), expected heterozygosity (HE), linkage disequilibrium (IAS), neighbor-joining analysis and Principal Coordinate Analysis. Datasets can also be formatted and exported for application in commonly used population genetic software including GENEPOP, Arlequin and STRUCTURE. To date, data from 10 countries, including 5 publicly available data sets have been shared with VivaxGEN. VivaxGEN is well placed to facilitate regional overviews of P. vivax transmission dynamics in different endemic settings and capable to be adapted for similar genetic studies of P. falciparum and other organisms.

  2. The mechanism of transactivation regulation due to polymorphic short tandem repeats (STRs) using IGF1 promoter as a model

    PubMed Central

    Chen, Holly Y.; Ma, Suk Ling; Huang, Wei; Ji, Lindan; Leung, Vincent H. K.; Jiang, Honglin; Yao, Xiaoqiang; Tang, Nelson L. S.

    2016-01-01

    Functional short tandem repeats (STR) are polymorphic in the population, and the number of repeats regulates the expression of nearby genes (known as expression STR, eSTR). STR in IGF1 promoter has been extensively studied for its association with IGF1 concentration in blood and various clinical traits and represents an important eSTR. We previously used an in-vitro luciferase reporter model to examine the interaction between STRs and SNPs in IGF1 promoter. Here, we further explored the mechanism how the number of repeats of the STR regulates gene transcription. An inverse correlation between the number of repeats and the extent of transactivation was found in a haplotype consisting of three promoter SNPs (C-STR-T-T). We showed that these adjacent SNPs located outside the STR were required for the STR to function as eSTR. The C allele of rs35767 provides a binding site for CCAAT/enhancer-binding-protein δ (C/EBPD), which is essential for the gradational transactivation property of eSTR and FOXA3 may also be involved. Therefore, we propose a mechanism in which the gradational transactivation by the eSTR is caused by the interaction of one or more transcriptional complexes located outside the STR, rather than by direct binding to a repeat motif of the STR. PMID:27910883

  3. "New turns from old STaRs": enhancing the capabilities of forensic short tandem repeat analysis.

    PubMed

    Phillips, Christopher; Gelabert-Besada, Miguel; Fernandez-Formoso, Luis; García-Magariños, Manuel; Santos, Carla; Fondevila, Manuel; Ballard, David; Syndercombe Court, Denise; Carracedo, Angel; Lareu, Maria Victoria

    2014-11-01

    The field of research and development of forensic STR genotyping remains active, innovative, and focused on continuous improvements. A series of recent developments including the introduction of a sixth dye have brought expanded STR multiplex sizes while maintaining sensitivity to typical forensic DNA. New supplementary kits complimenting the core STRs have also helped improve analysis of challenging identification cases such as distant pairwise relationships in deficient pedigrees. This article gives an overview of several recent key developments in forensic STR analysis: availability of expanded core STR kits and supplementary STRs, short-amplicon mini-STRs offering practical options for highly degraded DNA, Y-STR enhancements made from the identification of rapidly mutating loci, and enhanced analysis of genetic ancestry by analyzing 32-STR profiles with a Bayesian forensic classifier originally developed for SNP population data. As well as providing scope for genotyping larger numbers of STRs optimized for forensic applications, the launch of compact next-generation sequencing systems provides considerable potential for genotyping the sizeable proportion of nucleotide variation existing in forensic STRs, which currently escapes detection with CE. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Genetic mapping of X-linked mental retardation genes with short tandem repeat polymorphisms

    SciTech Connect

    Carpenter, N.J.; Pritchard, J.K.

    1994-09-01

    A number of loci for non-specific and syndromal forms of mental retardation (XLMR) have been mapped to certain regions of the X chromosome. As a prerequisite for molecular identification of several forms of XLMR, we have conducted linkage studies in five families. In family 1, the affected members have severe MR, microcephaly, foot anomalies and digital arches. The most likely location of the gene is between DXS983 and DXYS1. A maximum lod score of 3.0 was obtained with DXS986. In family 2, affected males with moderate MR, spasticity of the lower limbs, and clasped thumbs (probably have MASA syndrome). The gene maps between DXS297 and F8C with a maximum lod score with DXS52. In three families, genes were localized by recombinants but lod scores >2 were not achieved. Family 3 has affected males with moderate MR, microcephaly, short stature, widening of the nasal tip and brachydactyly. The obligate carrier females are normal. The gene was localized to Xp11.3-q21 between SYN1 and DXS1105. In family 4, the affected males have non-specific MR whereas the obligate carrier females are normal. The most likely location of the gene is Xp11.4-p22.1 between MAO-B amd DXS987. Family 5 has affected males with profound MR, seizures, and limb contractures and two of five carrier females with moderate MR and limb contractures. The gene maps between DXS1003 and DXS992 (Xp11.4-p22).

  5. A Systematic Evaluation of Short Tandem Repeats in Lipid Candidate Genes: Riding on the SNP-Wave

    PubMed Central

    Lamina, Claudia; Haun, Margot; Coassin, Stefan; Kloss-Brandstätter, Anita; Gieger, Christian; Peters, Annette; Grallert, Harald; Strauch, Konstantin; Meitinger, Thomas; Kedenko, Lyudmyla; Paulweber, Bernhard; Kronenberg, Florian

    2014-01-01

    Structural genetic variants as short tandem repeats (STRs) are not targeted in SNP-based association studies and thus, their possible association signals are missed. We systematically searched for STRs in gene regions known to contribute to total cholesterol, HDL cholesterol, LDL cholesterol and triglyceride levels in two independent studies (KORA F4, n = 2553 and SAPHIR, n = 1648), resulting in 16 STRs that were finally evaluated. In a combined dataset of both studies, the sum of STR alleles was regressed on each phenotype, adjusted for age and sex. The association analyses were repeated for SNPs in a 200 kb region surrounding the respective STRs in the KORA F4 Study. Three STRs were significantly associated with total cholesterol (within LDLR, the APOA1/C3/A4/A5/BUD13 gene region and ABCG5/8), five with HDL cholesterol (3 within CETP, one in LPL and one inAPOA1/C3/A4/A5/BUD13), three with LDL cholesterol (LDLR, ABCG5/8 and CETP) and two with triglycerides (APOA1/C3/A4/A5/BUD13 and LPL). None of the investigated STRs, however, showed a significant association after adjusting for the lead or adjacent SNPs within that gene region. The evaluated STRs were found to be well tagged by the lead SNP within the respective gene regions. Therefore, the STRs reflect the association signals based on surrounding SNPs. In conclusion, none of the STRs contributed additionally to the SNP-based association signals identified in GWAS on lipid traits. PMID:25050552

  6. Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): Transposable elements and short tandem repeats.

    PubMed

    Vera, Manuel; Bello, Xabier; Álvarez-Dios, Jose-Antonio; Pardo, Belen G; Sánchez, Laura; Carlsson, Jens; Carlsson, Jeanette E L; Bartolomé, Carolina; Maside, Xulio; Martinez, Paulino

    2015-12-01

    The flat oyster (Ostrea edulis) is one of the most appreciated molluscs in Europe, but its production has been greatly reduced by the parasite Bonamia ostreae. Here, new generation genomic resources were used to analyse the repetitive fraction of the oyster genome, with the aim of developing molecular markers to face this main oyster production challenge. The resulting oyster database, consists of two sets of 10,318 and 7159 unique contigs (4.8 Mbp and 6.8 Mbp in total length) representing the oyster's genome (WG) and haemocyte transcriptome (HT), respectively. A total of 1083 sequences were identified as TE-derived, which corresponded to 4.0% of WG and 1.1% of HT. They were clustered into 142 homology groups, most of which were assigned to the Penelope order of retrotransposons, and to the Helitron and TIR DNA-transposons. Simple repeats and rRNA pseudogenes, also made a significant contribution to the oyster's genome (0.5% and 0.3% of WG and HT, respectively).The most frequent short tandem repeats identified in WG were tetranucleotide motifs while trinucleotide motifs were in HT. Forty identified microsatellite loci, 20 from each database, were selected for technical validation. Success was much lower among WG than HT microsatellites (15% vs 55%), which could reflect higher variation in anonymous regions interfering with primer annealing. All microsatellites developed adjusted to Hardy-Weinberg proportions and represent a useful tool to support future breeding programmes and to manage genetic resources of natural flat oyster beds. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. The effect of an enzymatic bone processing method on short tandem repeat profiling of challenged bone specimens.

    PubMed

    Li, Richard; Klempner, Stacey

    2013-07-01

    Forensic analysis of DNA from bone can be important in investigating a variety of cases involving violent crimes and mass fatality cases. To remove the potential presence of co-mingled remains and to eliminate contaminants that interfere with forensic DNA analysis, the outer surface of the bone fragment must be cleaned. This study evaluated two methods for processing bone specimens prior to DNA isolation. Mechanical sanding and enzymatic trypsin methods were compared in this study. The effects of these methods on the yield of DNA isolated and the quality of DNA analysis were studied. It was revealed that comparable values of DNA yields between the two methods were observed. Additionally, to evaluate the capabilities of the cleaning effect of the bone processing methods, the presence of polymerase chain reaction inhibitors in the DNA extracts was monitored using the internal positive control. Similar Ct values of the internal positive control were observed as the DNA extracts of the trypsin method compared with that of the sanding method. The characterization of the effects of the trypsin treatment on the quality of DNA profiling was also carried out. To evaluate the integrity of the nuclear DNA isolated, the percentage of allele calls and the peak-height values of alleles of the short tandem repeat profiles were compared between the two methods. A paired-sample t-test revealed no significant difference between the two methods. Our data suggested that the trypsin method can be used as an alternative cleaning method to mechanical cleaning methods. This method can be used to process multiple samples simultaneously. This can be very important for achieving high-throughput DNA isolation through potential automation, which can be extremely valuable for situations such as the forensic DNA analysis of skeletal remains from mass fatality incidents. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  8. Genetic analysis of the short tandem repeat system D12S391 in the German and three Asian populations.

    PubMed

    Waiyawuth, W; Zhang, L; Rittner, C; Schneider, P M

    1998-06-08

    Genomic DNA samples from 222 individuals from Southern China, 154 individuals from Thailand, 100 individuals from Japan as well as from 124 German individuals were analysed for the short tandem repeat (STR) locus D12S391. Typing was carried out by polymerase chain reaction (PCR) amplification and subsequent polyacryramide gel electrophoresis and silver staining. In total, 12 alleles could be distinguished in two of the populations. Among Chinese, allele 19 is the most common with a frequency of 0.225, and among Germans, allele 18 with a frequency of 0.186. In the Thai population only 11 alleles could be distinguished and allele 19 is the most common with a frequency of 0.198. In Japanese, two previously unknown alleles 27 and 28 were detected, 14 alleles could be distinguished, and allele 18 is the most common with a frequency of 0.295. The expected exclusion chance for Chinese, Thai, Japanese and Germans in paternity cases is 0.67, 0.71, 0.67 and 0.75, respectively, and the discrimination power in identification cases is 0.95, 0.96, 0.95 and 0.97, respectively. Testing of the observed genotype distributions for Hardy-Weinberg equilibrium did not reveal any significant deviations. Segregation studies of 124 meioses among German families did not reveal any mutations at the D12S391 locus. In casework studies two variant alleles were detected with a trimeric repeat each (17.3 and 18.3), which have been confirmed by sequencing.

  9. Tri-allelic pattern of short tandem repeats identifies the murderer among identical twins and suggests an embryonic mutational origin.

    PubMed

    Wang, Li-Feng; Yang, Ying; Zhang, Xiao-Nan; Quan, Xiao-Liang; Wu, Yuan-Ming

    2015-05-01

    Monozygotic twins can be co-identified by genotyping of short tandem repeats (STRs); however, for distinguishing them, STR genotyping is ineffective, especially in the case of murder. Here, a rarely occurring tri-allelic pattern in the vWA locus (16, 18, 19) was identified only in the DNA of one identical twin, which could help to exonerate the innocent twin in a murder charge. This mutation was defined as primary through genotyping of the family and could be detected in blood, buccal and semen samples from the individual; however, two alternative allele-balanced di-allelic patterns (16, 18 or 16, 19) were detected in hair root sheath cells. Such a kind of segregation indicates a one-step mutation occurs in cell mitosis, which is after embryonic zygote formation and during the early development of the individual after the division of the blastocyte. Sequencing revealed the insertion between the allele 18 and 19 is a repeat unit of TAGA/TCTA (plus/minus strand), which belongs to "AGAT/ATCT"-based core repeats identified from all tri-allelic pattern reports recorded in the STR base and a detailed model was proposed for STR repeat length variation caused by false priming during DNA synthesis. Our model illustrates the possible origination of allele-balanced and unbalanced tri-allelic pattern, clarifies that the genotypes of parent-child mismatches, aberrant di-allelic patterns, and type 1 or 2 tri-allelic patterns should be considered as independent, but interconnected forms of STR mutation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  10. Y-short tandem repeat haplotype and paternal lineage of the Ezhava population of Kerala, south India

    PubMed Central

    Nair, Parvathy Seema; Geetha, Aswathy; Jagannath, Chippy

    2011-01-01

    Aim To analyze the haplotype of the Ezhava population of Kerala, south India, using 8 short tandem repeat (STR) loci on the Y chromosome and trace the paternal genetic lineage of the population. Methods Whole blood samples (n = 104) were collected from unrelated healthy men of the Ezhava population over a period of one year from October 2009. Genomic DNA was extracted by salting out method. All samples were genotyped for the 8 Y-STR loci by the AmpFiSTR Y-filer PCR Amplification Kit. The haplotype and allele frequencies were determined by direct counting and analyzed using Arlequin 3.1 software, and molecular variance was calculated with the Y-chromosome haplotype reference database online analysis tool, www.yhrd.org. Results Among the 104 examined haplotypes, we found 98 unique ones. The average gene diversity was 0.669, with the highest diversity of 0.9462 observed for the biallelic Y-STR marker DYS 385. The allele frequency among DYS loci varied between 0.0096 and 0.75. Out of the 104 haplotypes, 10 were identical to the Jat Sikh population of Punjab, which is the greatest number among the Indian populations, and 4 to the Turkish population, which is the greatest number among the European populations. According to the allele frequency of Y-STR, the Ezhavas were genetically more similar to the Europeans (60%) than to the East Asians (40%). Conclusion The vast majority of haplotypes were observed only once, reflecting the enormous genetic heterogeneity of the Ezhavas. Based on the genotype, the Ezhavas showed more resemblance to Jat Sikh population of Punjab and the Turkish populations than to the East Asians, hence indicating a paternal lineage of European origin. PMID:21674830

  11. Tissue identity testing of cancer by short tandem repeat polymorphism: pitfalls of interpretation in the presence of microsatellite instability.

    PubMed

    Much, Melissa; Buza, Natalia; Hui, Pei

    2014-03-01

    Tissue identity testing by short tandem repeat (STR) polymorphism offers discriminating power in resolving tissue mix-up or contamination. However, one caveat is the presence of microsatellite unstable tumors, in which genetic alterations may drastically change the STR wild-type polymorphism leading to unexpected allelic discordance. We examined how tissue identity testing results can be altered by the presence of microsatellite instability (MSI). Eleven cases of MSI-unstable (9 intestinal and 2 endometrial adenocarcinomas) and 10 cases of MSI-stable tumors (all colorectal adenocarcinomas) were included. All had been previously tested by polymerase chain reaction testing at 5 National Cancer Institute (NCI) recommended MSI loci and/or immunohistochemistry for DNA mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). Tissue identity testing targeting 15 STR loci was performed using AmpF/STR Identifiler Amplification. Ten of 11 MSI-unstable tumors demonstrated novel alleles at 5 to 12 STR loci per case and frequently with 3 or more allelic peaks. However, all affected loci showed identifiable germline allele(s) in MSI-high tumors. A wild-type allelic profile was seen in 7 of 10 MSI-stable tumors. In the remaining 3 cases, isolated novel alleles were present at a unique single locus in addition to germline alleles. Loss of heterozygosity was observed frequently in both MSI-stable (6/11 cases) and MSI-unstable tumors (8/10 cases). In conclusion, MSI may significantly alter the wild-type allelic polymorphism, leading to potential interpretation errors of STR genotyping. Careful examination of the STR allelic pattern, high index of suspicion, and follow-up MSI testing are crucial to avoid erroneous conclusions and subsequent clinical and legal consequences.

  12. Evaluation of factor VIII polymorphic short tandem repeat markers in linkage analysis for carrier diagnosis of hemophilia A

    PubMed Central

    Shrestha, Sabina; Dong, Sufang; Li, Zuhua; Huang, Zhuliang; Zheng, Fang

    2016-01-01

    Hemophilia A (HA) is the most common inherited X-linked recessive bleeding disorder caused by heterogeneous mutations in the factor VIII gene (FVIII). Diagnosis of the carrier is critical for preventing the birth of children affected by this coagulation disorder, which ultimately facilitates its management. Due to the heterogeneous nature of mutations, the large inversions and the complexity of the FVIII gene, direct recognition of the disease-associated mutation in HA is complex. Indirect linkage analysis using highly informative heterozygous polymorphic markers is an alternative method for determining the co-segregation of the mutant gene within a family for carrier detection of HA. The aim of the present study was to perform carrier diagnosis in a family with HA. Rapid multifluorescent polymerase chain reaction (PCR) was performed with six extragenic short tandem repeats (STRs), DXS1073, DXS15, DXS8091, DXS1227, DXS991, DXS993 and one intragenic marker, STR22 for linkage analysis in the HA family. All the STR markers employed in the present study were informative for linkages of pathogenic and healthy haplotypes among family members, particularly STR22, DXS1073 and DXS15. The STR marker, STR22, is within the FVIII gene while the DXS1073 and DXS15 markers are very close to the FVIII gene, where the chances of recombination are comparatively low, and provided the most accurate interpretation analysis, indicating that the proband's sister may have been the HA carrier. Rapid multifluorescent PCR using STR markers and linkage analysis was identified to be a simple method for performing HA carrier diagnosis. PMID:27446547

  13. Tandem ring-opening decarboxylation of cyclopropane hemimalonates with sodium azide: a short route to γ-aminobutyric acid esters.

    PubMed

    Emmett, Michael R; Grover, Huck K; Kerr, Michael A

    2012-08-03

    Cyclopropane hemimalonates, when treated with sodium azide, undergo a tandem ring-opening decarboxylation to produce γ-azidobutyric acids in good yields. These adducts were hydrogenated to form γ-aminobutyric acid (GABA) methyl esters.

  14. Analysis and interpretation of short tandem repeat microvariants and three-banded allele patterns using multiple allele detection systems.

    PubMed

    Crouse, C A; Rogers, S; Amiott, E; Gibson, S; Masibay, A

    1999-01-01

    The Palm Beach County Sheriffs Office (PBSO) Crime Laboratory and the Alabama Department of Forensic Sciences (ADFS) have validated and implemented analysis of short tandem repeat (STR) sequences on casework using silver staining kit and SYBR Green I detection systems and are presently validating fluorescently tagged STR alleles using the Hitachi FMBIO 100 instrument. Concurrently, the Broward County Sheriff's Office (BSO) Crime Laboratory is validating the ABI Prism310 Genetic Analyzer capillary electrophoresis STR detection system (ABI CE310) from Perkin Elmer Applied BioSystems. During the course of analyzing over 10,000 individuals for the STR loci CSF1PO, TPOX and THO1 (CTT) using silver staining for allele detection, 42 samples demonstrated alleles that were "off ladder," contained three-banded patterns at a single locus, or exhibited an apparent THO1 "9.3,10" allele pattern. PBSO, ADFS and BSO Crime Laboratories have collaborated on the verification of the allele patterns observed in these 42 samples using the following allele detection systems: (1) manual silver staining, (2) SYBR Green I staining, and/or (3) fluorescently tagged amplified products separated by polyacrylamide gel electrophoresis or capillary electrophoresis followed by laser detection. Regardless of the CTT allele detection system utilized, concordant results were obtained for 41 of the 42 samples. The only exception was a sample in which a wide band within the THO1 locus was identified as a THO1 "9.3, 10" genotype by silver staining kit and SYBR Green I staining but was verified to be a THO1 "9.3" homozygote by all other allele detection systems. Manual allele detection could readily identify microvariants, as a visual assessment of stained gels clearly shows that alleles do not migrate coincident with well-characterized allele size standards. As would be predicted, however, the manual detection systems did not provide adequate resolution to approximate the basepair size for off

  15. Case-control study of allele frequencies of 15 short tandem repeat loci in males with impulsive violent behavior.

    PubMed

    Yang, Chun; Ba, Huajie; Gao, Zhiqin; Zhao, Hanqing; Yu, Haiying; Guo, Wei

    2013-12-01

    Analysis of genetic polymorphisms in short tandem repeats (STRs) is an accepted method for detecting associations between genotype and phenotype but it has not previously been used in the study of the genetics of impulsive violent behavior. Compare the prevalence of different polymorphisms in 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) between men with a history of impulsive violence and male control subjects without a history of impulsive violence. The distributions of the alleles of the 15 STR loci were compared between 407 cases with impulsive violent behavior and 415 controls using AmpFlSTR(®) Identifiler™ kits. COMPARED TO CONTROLS, THE AVERAGE FREQUENCIES OF THE FOLLOWING ALLELES WERE SIGNIFICANTLY LOWER IN INDIVIDUALS WITH A HISTORY OF VIOLENT BEHAVIOR: allele 10 of TH01 (OR=0.29, 95%CI=0.16-0.52, p<0.0001,), allele 8 of TPOX (OR=0.71, 95%CI=0.58-0.86, p=0.0005), allele 9 of TPOX (OR=0.65, 95%CI=0.47-0.89, p=0.0072) and allele 14 of CSF1PO (OR=0.27, 95%CI=0.11-0.68, p=0.0035). One allele was significantly higher in cases than controls: allele 11 of TPOX (OR=1.79, 95%CI=1.45-2.22, p<0.0001). To the best of our knowledge, this is the first behavioral genetic study that clearly demonstrates a close relationship between specific genetic markers and impulsive aggression in non-psychiatric offenders. Further prospective work will be needed to determine whether or not the alleles identified can be considered risk factors for impulsive aggression and, if so, the underlying mechanisms that result in this relationship.

  16. Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation.

    PubMed

    Wang, Le; Zhao, Xing-Chun; Ye, Jian; Liu, Jin-Jie; Chen, Ting; Bai, Xue; Zhang, Jian; Ou, Yuan; Hu, Lan; Jiang, Bo-Wei; Wang, Feng

    2014-09-01

    Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to <500 base pairs, this library could provide universal templates for allelic ladder preparation. We prepared three different sets of allelic ladders for this locus TH01 and an updated version of an allelic ladder for the DNATyper(®)19 multiplex system using these plasmids to confirm the suitability of the library as a good source for allelic ladder preparation. Importantly, the authenticity of each construct was confirmed by bidirectional nucleotide sequencing and we report the repeat structures of the 259 STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  17. Authentication of newly established human esophageal squamous cell carcinoma cell line (YM-1) using short tandem repeat (STR) profiling method.

    PubMed

    Ayyoob, Khosravi; Masoud, Khoshnia; Vahideh, Kazeminejad; Jahanbakhsh, Asadi

    2016-03-01

    Cross-contamination during or early after establishment of a new cell line could result in the worldwide spread of a misidentified cell line. Therefore, newly established cell lines need to be authenticated by a reference standard method. This study was conducted to investigate the authenticity of a newly established epithelial cell line of human esophageal squamous cell carcinoma (ESCC) called YM-1 using short tandem repeat (STR) DNA profiling method. Primary human ESCC epithelial cells were cultured from the fresh tumor tissue of an adult female patient. Growth characteristics and epithelial originality of YM-1 cells were studied. Genomic DNA was isolated from YM-1 cells harvested at passage 22 and ESCC donor tumor sample on two different days to prevent probable DNA contamination. STR profiling was performed using AmpFℓSTR® Identifiler® Plus PCR Amplification Kit. To address whether YM-1 cells undergo genetic alteration as the passage number increases, STR profiling was performed again on harvested cells at passage 51. YM-1 cells grew as a monolayer with a population doubling time of 40.66 h. Epithelial originality of YM-1 cells was confirmed using ICC/IF staining of cytokeratins AE1/AE3. The STR profile of the ESCC donor tumor sample was the same with YM-1 cells at passage 22. However, STR profile of the donor tumor sample showed an off-ladder (OL) allele in their D7S820 locus. Also, re-profiling of YM-1 cells at passage 51 showed a loss of heterozygosity (LOH) at D18S51 locus. This suggests that long-term culture of cell lines may alter their DNA profile. Comparison of the DNA fingerprinting results in DSMZ, and ATCC STR profiling databases confirmed unique identity of YM-1 cell line. This study provides an easy, fast, and reliable procedure for authentication of newly established cell lines, which helps in preventing the spread of misidentified cells and improving the reproducibility and validity of experiments, consequently.

  18. Discovery of the first dual G-triplex/G-quadruplex stabilizing compound: a new opportunity in the targeting of G-rich DNA structures?

    PubMed

    Amato, Jussara; Pagano, Alessia; Cosconati, Sandro; Amendola, Giorgio; Fotticchia, Iolanda; Iaccarino, Nunzia; Marinello, Jessica; De Magis, Alessio; Capranico, Giovanni; Novellino, Ettore; Pagano, Bruno; Randazzo, Antonio

    2017-05-01

    Guanine-rich DNA motifs can form non-canonical structures known as G-quadruplexes, whose role in tumorigenic processes makes them attractive drug-target candidates for cancer therapy. Recent studies revealed that the folding and unfolding pathways of G-quadruplexes proceed through a quite stable intermediate named G-triplex. Virtual screening was employed to identify a small set of putative G-triplex ligands. The G-triplex stabilizing properties of these compounds were analyzed by CD melting assay. DSC, non-denaturing gel electrophoresis, NMR and molecular modeling studies were performed to investigate the interaction between the selected compound 1 and G-rich DNA structures. Cytotoxic activity of 1 was evaluated by MTT cell proliferation assay. The experiments led to the identification of a promising hit that was shown to bind preferentially to G-triplex and parallel-stranded G-quadruplexes over duplex and antiparallel G-quadruplexes. Molecular modeling results suggested a partial end-stacking of 1 to the external G-triad/G-tetrads as a binding mode. Biological assays showed that 1 is endowed with cytotoxic effect on human osteosarcoma cells. A tandem application of virtual screening along with the experimental investigation was employed to discover a G-triplex-targeting ligand. Experiments revealed that the selected compound actually acts as a dual G-triplex/G-quadruplex stabilizer, thus stimulating further studies aimed at its optimization. The discovery of molecules able to bind and stabilize G-triplex structures is highly appealing, but their transient state makes challenging their recognition. These findings suggest that the identification of ligands with dual G-triplex/G-quadruplex stabilizing properties may represent a new route for the design of anticancer agents targeting the G-rich DNA structures. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio. Copyright © 2016 Elsevier B

  19. Association between allelic variation due to short tandem repeats in tRNA gene of Entamoeba histolytica and clinical phenotypes of amoebiasis.

    PubMed

    Jaiswal, Virendra; Ghoshal, Ujjala; Mittal, Balraj; Dhole, Tapan N; Ghoshal, Uday C

    2014-05-01

    Genotypes of Entamoeba histolytica (E. histolytica) may contribute clinical phenotypes of amoebiasis such as amoebic liver abscess (ALA), dysentery and asymptomatic cyst passers state. Hence, we evaluated allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica and clinical phenotypes of amoebiasis. Asymptomatic cyst passers (n=24), patients with dysentery (n=56) and ALA (n=107) were included. Extracted DNA from stool (dysentery, asymptomatic cyst passers) and liver aspirate was amplified using 6 E. histolytica specific tRNA-linked STRs (D-A, A-L, N-K2, R-R, S-Q, and S(TGA)-D) primers. PCR products were subjected to sequencing. Association between allelic variation and clinical phenotypes was analyzed. A total of 9 allelic variations were found in D-A, 8 in A-L, 4 in N-K2, 5 in R-R, 10 in S(TAG)-D and 7 in S-Q loci. A significant association was found between allelic variants and clinical phenotypes of amoebiasis. This study reveals that allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica is associated different clinical outcome of amoebiasis. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Self-Assembly of G-Rich Oligonucleotides Incorporating a 3'-3' Inversion of Polarity Site: A New Route Towards G-Wire DNA Nanostructures.

    PubMed

    Oliviero, Giorgia; D'Errico, Stefano; Pinto, Brunella; Nici, Fabrizia; Dardano, Principia; Rea, Ilaria; De Stefano, Luca; Mayol, Luciano; Piccialli, Gennaro; Borbone, Nicola

    2017-08-01

    Obtaining DNA nanostructures with potential applications in drug discovery, diagnostics, and electronics in a simple and affordable way represents one of the hottest topics in nanotechnological and medical sciences. Herein, we report a novel strategy to obtain structurally homogeneous DNA G-wire nanostructures of known length, starting from the short unmodified G-rich oligonucleotide d(5'-CGGT-3'-3'-GGC-5') (1) incorporating a 3'-3' inversion of polarity site. The reported approach allowed us to obtain long G-wire assemblies through 5'-5' π-π stacking interactions in between the tetramolecular G-quadruplex building blocks that form when 1 is annealed in the presence of potassium ions. Our results expand the repertoire of synthetic methodologies to obtain new tailored DNA G-wire nanostructures.

  1. Guangdong and Florida populations of 'Candidatus Liberibacter asiaticus' distinguished by a genomic locus with short tandem repeats.

    PubMed

    Chen, J; Deng, X; Sun, X; Jones, D; Irey, M; Civerolo, E

    2010-06-01

    Huanglongbing (HLB) (yellow shoot disease) is a highly destructive disease that threatens citrus production worldwide. The disease was first observed in Guangdong, P.R. China, over 100 years ago, and was found in Florida, United States, in 2005. 'Candidatus Liberibacter asiaticus' has been associated with HLB in many citrus-growing regions around the world, including Guangdong and Florida. The global epidemiology of HLB, as well as management of the disease, relies on knowledge of 'Ca. L. asiaticus' populations in different geographical regions around the world. In this study, we identified a genetic marker containing small tandem repeats in the genome of 'Ca. L. asiaticus' and comparatively analyzed the tandem repeat numbers (TRNs) in 'Ca. L. asiaticus' populations from Guangdong and Florida. Analyses of TRNs showed that the bacterial population in Guangdong was different from that in Florida. The Guangdong population consisted predominately of strains with a TRN of 7 (TRN(7)) at a frequency of 47.6%. The Florida population consisted predominately of strains with a TRN of 5 (TRN(5)) at a frequency of 84.4%. TRNs ranged from 3 to 16. The apparent absence of TRNs of 9, 10, 11, and 12 separated the bacterial strains into two groups: TRNs < 10 (TRN(<10)) and TRNs > 10 (TRN(>10)). In Florida, TRN(<10) strains (103/109, or 94.5%) were widely distributed in all HLB-affected counties. TRN(>10) strains (6/109, or 5.5%) were found in central Florida. This is the first report documenting the differentiation of 'Ca. L. asiaticus' populations between Asia and North America and the possible presence of two differentially distributed genotypes of 'Ca. L. asiaticus' in Florida.

  2. Clinical utility of chimerism status assessed by lineage-specific short tandem repeat analysis: experience from four cases of allogeneic stem cell transplantation.

    PubMed

    Goh, Ri-Young; Cho, Sung-Suk; Song, Yoo-Jeong; Heo, Kyeong; Oh, Sung-Yong; Kim, Sung-Hyun; Kwon, Hyeok-Chan; Kim, Hyo-Jin; Han, Jin-Yeong

    2009-08-01

    Chimerism testing permits early prediction and documentation of successful engraftment, and also facilitates detection of impending graft rejection. In this study, we serially monitored chimerism status by short tandem repeat-based PCR in nucleated cells (NC), T cells and natural killer (NK) cells after myeloablative allogeneic stem cell transplantation (SCT). Four patients with myeloid malignancies showed discrepant chimerism results among those three fractions. Three patients had mixed chimerism (MC) of donor/host T cells at a time point around the onset of chronic graft-versus-host disease (GVHD). In two patients with disease relapse, MC of NK cells preceded a morphological relapse or NK cells showed a higher percentage of patient cells compared to NC. Therefore, our study shows that chimerism analysis in lineage-specific cells might be useful in predicting clinical outcome after allogeneic SCT in certain patients.

  3. Role of a short tandem leucine/arginine repeat in strong mutator phenotype acquisition in a clinical isolate of Salmonella Typhimurium.

    PubMed

    Le Bars, Hervé; Bousarghin, Latifa; Bonnaure-Mallet, Martine; Jolivet-Gougeon, Anne

    2013-01-01

    In this prospective study, a strong mutator strain of Salmonella Typhimurium was isolated from a collection of 130 human clinical strains of Salmonella. Sequence analysis of the mutS, mutL, and mutH genes, which encode three proteins that are essential for initiation of methyl-directed DNA mismatch repair, revealed insertion of a short tandem repeat (STR) of leucine/alanine in the histidine kinase-like ATPase domain of MutL. The role of this STR in the acquisition of the strong mutator phenotype was confirmed by the construction of an isogenic mutant (6bpinsmutL) from a normomutator strain of Salmonella Heidelberg. This result adds to the sparse body of knowledge about strong mutators and highlights the role of this STR as a hotspot for the acquisition of a strong mutator phenotype in Salmonella.

  4. DNA extraction for short tandem repeat typing from mixed samples using anti-human leukocyte CD45 and ABO blood group antibodies.

    PubMed

    Yano, Shizue; Honda, Katsuya; Kaminiwa, Junko; Nishi, Takeki; Iwabuchi, Yayoi; Sugano, Yukiko; Kurosu, Akira; Suzuki, Yasuhito

    2014-05-01

    DNA testing from mixed cell samples can be difficult to use successfully in criminal investigations. Here, we present a method for the extraction of DNA from mixed bloodstains involving plural contributors, after antibody-microbead captured cell separation. This method, together with the multiplex short tandem repeat typing presented, has proven highly successful in the recovery of DNA profiles corresponding to the ABO blood type. Methodological steps include magnetic separation using leukocyte specific CD45 antibody-coated microbeads and centrifugal separation of leukocyte agglutination by ABO antibody. The detection results of variable mixed ratio showed that the target DNA was detected accurately as low as 1:512 mixed ratio, regardless of the large amount of the background DNA present. The method presented here is applicable to PCR-based identification for various kinds of mixed samples.

  5. Short tandem target mimic: a long journey to the engineered molecular landmine for selective destruction/blockage of microRNAs in plants and animals.

    PubMed

    Tang, Guiliang; Tang, Xiaoqing

    2013-06-20

    MicroRNAs (miRNAs) are a population of highly conserved specific small ribo-regulators that negatively regulate gene expressions in both plants and animals. They play a key role in post-transcriptional gene regulation by destabilizing the target gene transcripts or blocking protein translation from them. Interestingly, these negative regulators are largely compromised by an upstream layer of negative regulators "target mimics" found in plants or "endogenous competing RNAs" revealed recently in animals. These endogenous regulatory mechanisms of "double negatives making a positive" have now been developed into a key strategy in the study of small RNA functions. This review presents some reflections on the long journey to the short tandem target mimic (STTM) for selective destruction/blockage of specific miRNAs in plants and animals, and the potential applications of STTM are discussed. Copyright © 2013. Published by Elsevier Ltd.

  6. Diversity of Y-short tandem repeats in the representative sample of the population of Canton Sarajevo residents, Bosnia and Herzegovina.

    PubMed

    Cenanović, Merisa; Pojskić, Naris; Kovacević, Lejla; Dzehverović, Mirela; Cakar, Jasmina; Musemić, Dzenisa; Marjanović, Damir

    2010-06-01

    In our previous population study, we have used twelve Y-chromosomal short tandem repeats loci incorporated in the PowerPlex Y System to determine Y-STR diversity in B&H human population. With intent to obtain additional verification of the previously obtained results as well as to establish specific reference for a local B&H population, we have decided to test DNA samples collected from 100 unrelated healthy male Canton Sarajevo residents (from Sarajevo region) for the same twelve Y-linked short tandem repeats loci. Qiagen DNeasy Tissue Kit (Qiagen, GmbH, Hilden, Germany) was used for DNA extraction from buccal swabs and PowerPlex Y System (Promega Corp., Madison, WI) has been used to simultaneously amplify Y-STR loci by PCR. PowerPlex Y System includes 12 STR loci: DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439. The total PCR reaction volume was 5 microL. PCR amplifications were carried out in PE GeneAmp PCR System Thermal Cycler (ABI). Electrophoresis of the amplification products was preformed on an ABI PRISM 310 genetic analyzer (ABI, Foster City, CA) according to the manufacturer's recommendations. The raw data were compiled and analyzed using the accessory software: ABI PRISM Data Collection Software and Genemapper version 3.2. In addition, we have compared the obtained "Sarajevo" dataset with the data previously generated for the entire Bosnian and Herzegovinian population, as well as with the available data on geographically close (neighboring) European populations. The results of this study will be used as guidelines in additional improving of research into genetic relationship among recent local B&H populations, both isolated and open, which is a long-term project in our country.

  7. A new variant of endemic pemphigus foliaceus in El-Bagre, Colombia: the Hardy-Weinberg-Castle law and linked short tandem repeats

    PubMed Central

    Abreu-Velez, Ana María; Robles, Edinson Villa; Howard, Michael S.

    2009-01-01

    Background: We reported a new variant of endemic pemphigus foliaceus in El Bagre, Colombia. Aims: Our study performed Complex Segregation Analysis (CSA) and short tandem repeats to discriminate between environmental and/or genetic factors in this disorder. Materials and Methods: The CSA analysis was carried out according to the unified model, implemented using the transmission probabilities implemented in the computer program POINTER, and evaluated by using a software package for population genetic data analysis (GDA), Arlequin. We performed pedigree analyses by using Cyrillic 2.1 software, with a total of 30 families with 50 probands (47 males and 3 females) tested. In parallel to the CSA, we tested for the presence of short tandem repeats from HLA class II, DQ alpha 1, involving the gene locus D6S291 by using the Hardy-Weinberg- Castle law. Results Our results indicate that the best model of inheritance in this disease is a mixed model, with multifactorial effects within a recessive genotype. Two types of possible segregation patterns were found; one with strong recessive penetrance in families whose phenotype is more Amerindian-like, and another of possible somatic mutations. Conclusion: The penetrance of 10% or less in female patients 60 years of age or older indicates that hormones could protect younger females. The greatest risk factor for men being affected by the disorder was the NN genotype. These findings are only possible due to somatic mutations, and/or strong environmental effects. We also found a protective role for two genetic loci (D6S1019 AND D6S439) in the control group. PMID:22666691

  8. Microevolution of pandemic Vibrio parahaemolyticus assessed by the number of repeat units in short sequence tandem repeat regions.

    PubMed

    García, Katherine; Gavilán, Ronnie G; Höfle, Manfred G; Martínez-Urtaza, Jaime; Espejo, Romilio T

    2012-01-01

    The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain but this requires knowing the rate and mechanism of VNTRs' variation. Our study of mutants obtained after serial cultivation of clones showed that mutation rates of the six VNTRs examined are on the order of 10(-4) mutant per generation and that difference increases by stepwise addition of single mutations. The single stepwise mutation (SSM) was deduced because mutants with 1, 2, 3, or more repeat unit deletions or insertions follow a geometric distribution. Plausible phylogenetic trees are obtained when, according to SSM, the genetic distance between clusters with different number of repeats is assessed by the absolute differences in repeats. Using this approach, mutants originated from different isolates of pandemic V. parahaemolyticus after serial cultivation are clustered with their parental isolates. Additionally, isolates of pandemic V. parahaemolyticus from Southeast Asia, Tokyo, and northern and southern Chile are clustered according their geographical origin. The deepest split in these four populations is observed between the Tokyo and southern Chile populations. We conclude that proper phylogenetic relations and successful tracing of pandemic V. parahaemolyticus requires measuring the differences between isolates by the absolute number of repeats in the VNTRs considered.

  9. Use of a novel panel of nine short tandem repeats for exact and high-resolution fingerprinting of Aspergillus fumigatus isolates.

    PubMed

    de Valk, Hanneke A; Meis, Jacques F G M; Curfs, Ilse M; Muehlethaler, Konrad; Mouton, Johan W; Klaassen, Corné H W

    2005-08-01

    Here we describe a new panel of short tandem repeats (STRs) for a novel exact typing assay that can be used to discriminate between Aspergillus fumigatus isolates. A total of nine STR markers were selected from available genomic A. fumigatus sequences and were divided into three multicolor multiplex PCRs. Each multiplex reaction amplified three di-, tri-, or tetranucleotide repeats, respectively. All nine STR markers were used to analyze 100 presumably unrelated A. fumigatus isolates. For each marker, between 11 and 37 alleles were found in this population. One isolate proved to be a mixture of at least two different isolates. With the remaining 99 isolates, 96 different fingerprinting profiles were obtained. The Simpson's diversity index for the individual markers ranged from 0.77 to 0.97. The diversity index for the multiplex combination of di-, tri-, and tetranucleotide repeats ranged from 0.9784 to 0.9968. The combination of all nine markers yielded a Simpson's diversity index of 0.9994, indicative of the high discriminatory power of these new loci. In theory, this panel of markers is able to discriminate between no less than 27 x 10(9) different genotypes. The multicolor multiplex approach allows large numbers of markers to be tested in a short period of time. The exact nature of the assay combines high reproducibility with the easy exchange of results and makes it a very suitable tool for large-scale epidemiological studies.

  10. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER).

    PubMed

    Bodner, Martin; Bastisch, Ingo; Butler, John M; Fimmers, Rolf; Gill, Peter; Gusmão, Leonor; Morling, Niels; Phillips, Christopher; Prinz, Mechthild; Schneider, Peter M; Parson, Walther

    2016-09-01

    The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups. It has been demonstrated with databases of haploid markers (EMPOP for mitochondrial mtDNA, and YHRD for Y-chromosomal loci) that centralized quality control and data curation is essential to minimize error. The concepts employed for quality control involve software-aided likelihood-of-genotype, phylogenetic, and population genetic checks that allow the researchers to compare novel data to established datasets and, thus, maintain the high quality required in forensic genetics. Here, we present STRidER (http://strider.online), a publicly available, centrally curated online allele frequency database and quality control platform for autosomal STRs. STRidER expands on the previously established ENFSI DNA WG STRbASE and applies standard concepts established for haploid and autosomal markers as well as novel tools to reduce error and increase the quality of autosomal STR data. The platform constitutes a significant improvement and innovation for the scientific community, offering autosomal STR data quality control and reliable STR genotype estimates.

  11. PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

    PubMed

    Pereira, Luísa; Alshamali, Farida; Andreassen, Rune; Ballard, Ruth; Chantratita, Wasun; Cho, Nam Soo; Coudray, Clotilde; Dugoujon, Jean-Michel; Espinoza, Marta; González-Andrade, Fabricio; Hadi, Sibte; Immel, Uta-Dorothee; Marian, Catalin; Gonzalez-Martin, Antonio; Mertens, Gerhard; Parson, Walther; Perone, Carlos; Prieto, Lourdes; Takeshita, Haruo; Rangel Villalobos, Héctor; Zeng, Zhaoshu; Zhivotovsky, Lev; Camacho, Rui; Fonseca, Nuno A

    2011-09-01

    Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

  12. Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina.

    PubMed

    Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

    2014-10-01

    To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other.

  13. Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina

    PubMed Central

    Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

    2014-01-01

    Aim To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. Methods This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Results Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Conclusion Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other. PMID:25358886

  14. Determination of mini-short tandem repeat (miniSTR) loci by using the combination of polymerase chain reaction (PCR) and microchip electrophoresis.

    PubMed

    Lin, Xuexia; Wu, Jing; Li, Haifang; Wang, Zhihua; Lin, Jin-Ming

    2013-09-30

    In this work, a simple and convenient method for the detection of mini-short tandem repeat (miniSTR) loci has been developed by the combination of polymerase chain reaction (PCR) and microchip electrophoresis (MCE). Degraded or inhibitor DNA greatly limited STR loci analysis. Therefore, The proper primers was designed as close as possible to the STRs region to produce smaller size STRs, and made the assay suitable for the destroyed samples. Two annealing temperatures were applied in one PCR procedure and the corresponding cycle numbers were studied to improve the sensitivity of PCR reaction. Under optimal conditions, 0.001 ng DNA templates were enough to generate miniSTRs. The relative standard deviations (n=3) of the size fifteen miniSTRs from DNA9947A ranged from 0.49% to 4.41%. The RSDs of concentrations were between 0.94% and 4.95%. Fifteen miniSTRs were also well produced from human hair, indicating that the method has great potential application in criminal identification and paternity testing. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12.

    PubMed Central

    Levinson, G; Gutman, G A

    1987-01-01

    Slipped-strand mispairing (SSM) may play an major role in repetitive DNA sequence evolution by generating large numbers of short frameshift mutations within simple tandem repeats. Here we examine the frequency and size spectrum of frameshifts generated within poly-CA/TG sequences inserted into bacteriophage M13 in Escherichia coli hosts. The frequency of detectable frameshifts within a 40 bp tract of poly-CA/TG is greater than one percent and increases more than linearly with length, being lower by a factor of four in a 22 bp target sequence. The frequency increases more than 13-fold in mutL and mutS host cells, suggesting that a high proportion of frameshift events are normally repaired by methyl-directed mismatch repair. Of the 87 sequenced frameshifts in this study, 96% result from deletion or insertion of only or two 2 bp repeat units. The most frequent events are 2 bp deletions, 2 bp insertions, and 4 bp deletions, the relative frequencies of these events being about 18:6:1. PMID:3299269

  16. [Constructing standard allelic ladders for four short tandem repeat loci and employing them in a population study on Han Nationality of Chengdu in China].

    PubMed

    Deng, Jian-qiang; Ying, Bing-wu; Shi, Mei-sen; Yan, Jing; Jia, Zheng-jun; Li, Ying-bi; Wu, Jin; Zhang, Ji; Hou, Yi-ping

    2005-02-01

    To solve the problems in the accuracy and standardization of short tandem repeats-polymerase chain reaction (STR-PCR) typing, the authors adopted the molecular clone technology in producing the standard allelic ladders of D1S1676, D2S2735, D11S1977 and D22S444 loci and applied them in a population study on the Hans in Chengdu, China. PCR was used to produce several different allelic fragments of these loci. PCR products were eluted from the gel and re-amplified by PCR. The purified allelic fragments were then blunt-end subcloned individually into the pGEMR-T plasmid vectors and the recombinant were transfected into competent E.coli DH5alpha TM cells. The results of sequencing confirmed that the size and the construction of the inserts were correct. The recombinant plasmids DNA with the inserts were then used as template for re-amplification to generate the four loci standard ladders. The authors succeeded in producing large quantity of standard allelic ladder of these four loci, with which the genetic polymorphisms of these loci in Chengdu Han population of China were studied. This method is of high value for forensic DNA typing to construct standard ladders. D1S1676, D2S2735 loci are robust for forensic analysis in Chinese Han population, whereas the value of D11S1977 and D22S444 loci is limited.

  17. Evaluation of 14 Y-chromosomal Short Tandem Repeat Haplotype with Focus on DYS449, DYS456, and DYS458: Czech Population Sample

    PubMed Central

    Ehler, Edvard; Marvan, Richard; Vanek, Daniel

    2010-01-01

    Aim To evaluate the novel triplex polymerase chain reaction (PCR) assay for the analysis of polymorphic Y-chromosomal short tandem repeat loci (Y-STR). Methods A total of 14 Y-STR loci was analyzed. Allele frequencies for 3 tetrameric Y-STR loci (DYS449, DYS456, and DYS458) and extended haplotype loci typed by Y-PLEXTM 12 system were investigated in a sample of 50 unrelated healthy Czech male donors. We computed the relevant intra-population statistic parameters for our data (gene diversity, average gene diversity over loci, and mean number of pairwise differences) and compared our sample set with other Central European populations using RST pairwise genetic distance. Results We focused on the comparison of genetic diversity between the Y-STR extended haplotype loci and that of the 3 additional loci, and on the benefit of using DYS449, DYS456, and DYS458 in forensic and population genetics applications. Total gene diversity in our sample set was 0.998367 when using all 14 loci. Our data analysis revealed very high genetic diversity at DYS449 locus (0.876735), which surpasses even the diversity at DYS385a/b (0.819592). Population comparison showed no difference between Czech, Bavarian, Austrian, and Saxon sample set. A minor difference was found between Czech and Polish sample set. Conclusion Typing of 3 Y-chromosomal microsatellite polymorphisms may provide a useful complement to already established sets of Y-STRs. PMID:20162746

  18. Determination of short chain chlorinated paraffins in water by stir bar sorptive extraction-thermal desorption-gas chromatography-triple quadrupole tandem mass spectrometry.

    PubMed

    Tölgyessy, P; Nagyová, S; Sládkovičová, M

    2017-03-08

    A simple, robust, sensitive and environment friendly method for the determination of short chain chlorinated paraffins (SCCPs) in water using stir bar sorptive extraction (SBSE) coupled to thermal desorption-gas chromatography-triple quadrupole tandem mass spectrometry (TD-GC-QqQ-MS/MS) was developed. SBSE was performed using 100mL of water sample, 20mL of methanol as a modifier, and a commercial sorptive stir bar (with 10mm×0.5mm PDMS layer) during extraction period of 16h. After extraction, the sorptive stir bar was thermally desorbed and online analysed by GC-MS/MS. Method performance was evaluated for MilliQ and surface water spiked samples. For both types of matrices, a linear dynamic range of 0.5-3.0μgL(-1) with correlation coefficients >0.999 and relative standard deviations (RSDs) of the relative response factors (RRFs) <12% was established. The limits of quantification (LOQs) of 0.06 and 0.08μgL(-1), and the precision (repeatability) of 6.4 and 7.7% (RSDs) were achieved for MilliQ and surface water, respectively. The method also showed good robustness, recovery and accuracy. The obtained performance characteristics indicate that the method is suitable for screening and monitoring and compliance checking with environmental quality standards (EQS, set by the EU) for SCCPs in surface waters.

  19. Genetic polymorphisms of short tandem repeat loci D13S305, D13S631 and D13S634 in the Han population of Tianjin, China

    PubMed Central

    SHI, YUNFANG; LI, XIAOZHOU; JU, DUAN; LI, YAN; ZHANG, XIULING; ZHANG, YING

    2015-01-01

    Short tandem repeat (STR) markers, also known as microsatellites, are extensively used in mapping studies, forensics and disease diagnosis due to their small dimension and low mutation and high polymorphism rates. In recent years quantitative fluorescence polymerase chain reaction (QF-PCR) has been successfully used to amplify STR markers in the prenatal diagnosis of common chromosomal abnormalities. This method provides a diagnosis of common aneuploidies 24–48 h after sampling with low error rates and cost; however, the size of different alleles, frequency, heterozygosity and distribution of STR markers vary among different populations. In the present study three STR markers, D13S305, D13S631 and D13S634, on chromosome 13 were analyzed in 350 unrelated individuals (200 males and 150 females) from the Han population of Tianjin, China using QF-PCR. Eleven, seven and 11 alleles of each marker were observed, respectively. The frequencies of the genotypes were in good agreement with Hardy-Weinberg equilibrium (P>0.05). The results showed that these three STR markers were highly polymorphic in the Han population of Tianjin, China. The study has provided basic data for use in the prenatal diagnosis of Patau syndrome. PMID:26622392

  20. Genetic polymorphisms of short tandem repeat loci D13S305, D13S631 and D13S634 in the Han population of Tianjin, China.

    PubMed

    Shi, Yunfang; Li, Xiaozhou; Ju, Duan; Li, Yan; Zhang, Xiuling; Zhang, Ying

    2015-08-01

    Short tandem repeat (STR) markers, also known as microsatellites, are extensively used in mapping studies, forensics and disease diagnosis due to their small dimension and low mutation and high polymorphism rates. In recent years quantitative fluorescence polymerase chain reaction (QF-PCR) has been successfully used to amplify STR markers in the prenatal diagnosis of common chromosomal abnormalities. This method provides a diagnosis of common aneuploidies 24-48 h after sampling with low error rates and cost; however, the size of different alleles, frequency, heterozygosity and distribution of STR markers vary among different populations. In the present study three STR markers, D13S305, D13S631 and D13S634, on chromosome 13 were analyzed in 350 unrelated individuals (200 males and 150 females) from the Han population of Tianjin, China using QF-PCR. Eleven, seven and 11 alleles of each marker were observed, respectively. The frequencies of the genotypes were in good agreement with Hardy-Weinberg equilibrium (P>0.05). The results showed that these three STR markers were highly polymorphic in the Han population of Tianjin, China. The study has provided basic data for use in the prenatal diagnosis of Patau syndrome.

  1. Comparison of the Frequency of Y-short Tandem Repeats Markers between Sadat and Non-Sadat Populations in Isfahan Province of Iran

    PubMed Central

    Seyedebrahimi, Reihaneh; Esfandiari, Ebrahim; Rashidi, Bahman; Salehi, Rasoul; Dahghi, Ali Gholami; Dabiri, Shahriar; Kheirollahi, Majid

    2017-01-01

    Background: Y chromosome is one of the two sex chromosomes and is male specific. Due to limited genetic exchange, the main part of that is passed virtually unchanged from one generation to next generation. The short tandem repeats (STRs) are almost constant on chromosomes that make them as an appropriate factor for use in population genetic studies. In this study, we used the STRs of Y chromosome markers in Sadat families and comparison with other families was investigated. Materials and Methods: In this study, sampling was done from fifty unrelated males of Sadat families and fifty unrelated males of non-Sadat families. After the extraction of DNA from blood samples and primer design, polymerase chain reaction (PCR) was performed for each primer pairs separately. The PCR products were run on agarose gel that followed by running on polyacrylamide gel for better resolution. In addition, some sequenced samples were used as identified markers to determine the length of other alleles in polyacrylamide gel. Results: The survey of six STR in two case and control groups was carried out, and analysis revealed that the frequency of some alleles is different in case group compared to control group. Allele frequency of the markers DYS392, DYS393, DYS19, DYS390, DYS388, and DYS437 on the Y chromosome in Sadat families was quite different in comparison with other families. Conclusions: The reason for these differences in allele frequencies of the Sadat family in comparison with other families is having a common ancestor.

  2. Influence of fluorophor dye labels on the migration behavior of polymerase chain reaction--amplified short tandem repeats during denaturing capillary electrophoresis.

    PubMed

    Hahn, M; Wilhelm, J; Pingoud, A

    2001-08-01

    The determination of the length of polymerase chain reaction (PCR)-amplified short tandem repeats (STRs) by denaturing capillary electrophoresis (CE) is a standard procedure for purposes of genotyping. We show that dye-specific mobility anomalies exist for 5'-fluorophor-labelled single-stranded DNA (ssDNA) fragments in CE using the performance-optimized polymer 4 (POP4) buffer sieving matrix, containing the entangled poly(N,N-dimethylacrylamide) polymer, urea, and 2-pyrrolidinone. The dye-specific retardation effects relative to coseparated GeneScan-500 [TAMRA] standard fragments can lead to wrong genotyping, even for allele-specific fragments of pentanucleotide STRs, when comparing the relative calculated sizes of identical fragments, labelled with rhodamine (ROX, TAMRA) or fluorescein dyes (FAM, 6-FAM, HEX, JOE, NED, TET): The size of fluorescein dye-labelled fragments of appr. 100 b in length appears to be smaller by up to 6.5 b. This effect becomes more dramatic with decreasing size: a 6-FAM-labelled 24-mer oligonucleotide appeared to be smaller by 11 b. In contrast, in classical urea/polyacrylamide slab-gel electrophoresis only a small dye-specific retardation of identical fragments is observed. The dye-specific effects are superimposed by weaker size and sequence-dependent anomalies of fragment mobility. Therefore, in denaturing CE the coseparation of a defined allele ladder labelled with the same dye as the unknown sample fragments remains the method of choice for accurate genotyping.

  3. Identification of exhumed remains of fire tragedy victims using conventional methods and autosomal/Y-chromosomal short tandem repeat DNA profiling.

    PubMed

    Calacal, Gayvelline C; Delfin, Frederick C; Tan, Michelle Music M; Roewer, Lutz; Magtanong, Danilo L; Lara, Myra C; Fortun, Raquel dR; De Ungria, Maria Corazon A

    2005-09-01

    In a fire tragedy in Manila in December 1998, one of the worst tragic incidents which resulted in the reported death of 23 children, identity could not be established initially resulting in the burial of still unidentified bodies. Underscoring the importance of identifying each of the human remains, the bodies were exhumed 3 months after the tragedy. We describe here our work, which was the first national case handled by local laboratories wherein conventional and molecular-based techniques were successfully applied in forensic identification. The study reports analysis of DNA obtained from skeletal remains exposed to conditions of burning, burial, and exhumation. DNA typing methods using autosomal and Y-chromosomal short tandem repeat (Y-STR) markers reinforced postmortem examinations using conventional identification techniques. The strategy resulted in the identification of 18 out of the 21 human remains analyzed, overcoming challenges encountered due to the absence of established procedures for the recovery of mass disaster remains. There was incomplete antemortem information to match the postmortem data obtained from the remains of 3 female child victims. Two victims were readily identified due to the availability of antemortem tissues. In the absence of this biologic material, parentage testing was performed using reference blood samples collected from parents and relatives. Data on patrilineal lineage based on common Y-STR haplotypes augmented autosomal DNA typing, particularly in deficiency cases.

  4. An Empirical Comparison of Short Tandem Repeats (STRs) and Single Nucleotide Polymorphisms (SNPs) for Relatedness Estimation in Chinese Rhesus Macaques (Macaca mulatta)

    PubMed Central

    Ross, Cody T.; Weise, Jessica A.; Bonnar, Sarah; Nolin, David; Trask, Jessica Satkoski; Smith, David Glenn; Ferguson, Betsy; Ha, James; Kubisch, H. Michael; Vinson, Amanda; Kanthaswamy, Sree

    2015-01-01

    We compare the effectiveness of short tandem repeat (STR) and single nucleotide polymorphism (SNP) genotypes for estimating pairwise relatedness, using molecular data and pedigree records from a captive Chinese rhesus macaque population at the California National Primate Research Center. We find that a panel of 81 SNPs is as effective at estimating first-order kin relationships as a panel of 14 highly polymorphic STRs. We note, however, that the selected STRs provide more precise predictions of relatedness than the selected SNPs, and may be preferred in contexts that require the discrimination of kin related more distantly than first-order relatives. Additionally, we compare the performance of three commonly used relatedness estimation algorithms, and find that the Wang [2002] algorithm outperforms other algorithms when analyzing STR data, while the Queller and Goodnight [1994] algorithm outperforms other algorithms when analyzing SNP data. Future research is needed to address the number of SNPs required to reach the discriminatory power of a standard STR panel in relatedness estimation for primate colony management. PMID:24273109

  5. Effect of different DNA concentration methods on performance of non-invasive fetal y-chromosomal short tandem repeat profiling from maternal plasma.

    PubMed

    Repiská, Gabriela; Sedláčková, Tatiana; Szemes, Tomáš; Minárik, Gabriel

    2015-01-01

    The accuracy and reliability of detection of free fetal DNA in plasma of pregnant women can be significantly improved by increasing the overall DNA concentration following the isolation from maternal plasma. The aim of our study was to compare DNA concentration methods on samples with free fetal DNA. DNA isolated from plasma samples of pregnant women carrying a male fetus were concentrated by 3 different methods: vacuum concentration, centrifugal filters and spin columns. Their performance was evaluated using PCR-based Y-chromosomal short tandem repeat (Y-STR) genotyping of the fetus. A statistically significant difference was found between the 3 tested methods (F = 15.57, p < 0.0001). Using vacuum concentration 85.3% of paternally inherited Y-STR alleles were correctly identified. A significantly smaller proportion of alleles was correctly identified in samples concentrated by centrifugal filters and spin columns - 75.9 and 66.5%, respectively. The highest proportion of paternally inherited Y-STR alleles was found in samples concentrated with the use of vacuum concentration. This concentration procedure does not require further handling of the sample either, which is an advantage because it avoids potential sample contamination. On the other hand, when automation is considered, vacuum concentration is less suitable because of an uneven and unpredictable sample evaporation rate. © 2014 S. Karger AG, Basel.

  6. The RNase P RNA from cyanobacteria: short tandemly repeated repetitive (STRR) sequences are present within the RNase P RNA gene in heterocyst-forming cyanobacteria.

    PubMed Central

    Vioque, A

    1997-01-01

    The RNase P RNA gene (rnpB) from 10 cyanobacteria has been characterized. These new RNAs, together with the previously available ones, provide a comprehensive data set of RNase P RNA from diverse cyanobacterial lineages. All heterocystous cyanobacteria, but none of the non-heterocystous strains analyzed, contain short tandemly repeated repetitive (STRR) sequences that increase the length of helix P12. Site-directed mutagenesis experiments indicate that the STRR sequences are not required for catalytic activity in vitro. STRR sequences seem to have recently and independently invaded the RNase P RNA genes in heterocyst-forming cyanobacteria because closely related strains contain unrelated STRR sequences. Most cyanobacteria RNase P RNAs lack the sequence GGU in the loop connecting helices P15 and P16 that has been established to interact with the 3'-end CCA in precursor tRNA substrates in other bacteria. This character is shared with plastid RNase P RNA. Helix P6 is longer than usual in most cyanobacteria as well as in plastid RNase P RNA. PMID:9254706

  7. Monitoring of hematopoietic chimerism after transplantation for pediatric myelodysplastic syndrome: real-time or conventional short tandem repeat PCR in peripheral blood or bone marrow?

    PubMed

    Willasch, Andre M; Kreyenberg, Hermann; Shayegi, Nona; Rettinger, Eva; Meyer, Vida; Zabel, Marion; Lang, Peter; Kremens, Bernhard; Meisel, Roland; Strahm, Brigitte; Rossig, Claudia; Gruhn, Bernd; Klingebiel, Thomas; Niemeyer, Charlotte M; Bader, Peter

    2014-12-01

    Quantitative real-time PCR (qPCR) has been proposed as a highly sensitive method for monitoring hematopoietic chimerism and may serve as a surrogate marker for the detection of minimal residual disease minimal residual disease in myelodysplastic syndrome (MDS), until specific methods of detection become available. Because a systematic comparison of the clinical utility of qPCR with the gold standard short tandem repeat (STR)-PCR has not been reported, we retrospectively measured chimerism by qPCR in 54 children transplanted for MDS in a previous study. Results obtained by STR-PCR in the initial study served as comparison. Because the detection limit of qPCR was sufficiently low to detect an autologous background, we defined the sample as mixed chimera if the proportion of recipient-derived cells exceeded .5%. The true positive rates were 100% versus 80% (qPCR versus STR-PCR, not significant), and mixed chimerism in most cases was detected earlier by qPCR than by STR-PCR (median, 31 days) when chimerism was quantified concurrently in peripheral blood and bone marrow. Both methods revealed a substantial rate of false positives (22.7% versus 13.6%, not significant), indicating the importance of serial testing of chimerism to monitor its progression. Finally, we propose criteria for monitoring chimerism in pediatric MDS with regard to the subtypes, specimens, PCR method, and timing of sampling.

  8. Genetic variation observed at three tetrameric short tandem repeat loci HumTHO1, TPOX, and CSF1PO--in five ethnic population groups of northeastern India.

    PubMed

    Ranjan, D; Kashyap, V K

    2001-01-01

    This paper portrays the genetic variation observed at three tetrameric short tandem repeat (STR) loci HumTHO1, TPOX, and CSF1PO in five ethnic population groups from northeastern India. The study also specifies the suitability of use of these markers for forensic testing. The populations studied included three tribal groups (Kuki, Naga and Hmar), one Mongoloid caste group (Meitei), and a religious caste group (Manipuri Muslims). The loci were highly polymorphic in the populations, and all loci met Hardy-Weinberg expectations. No evidence for association of alleles among the loci was detected. The probability of match for the three loci of the most frequent genotype in the five population groups ranged between 2.6 x 10(-4) and 6.6 x 10(-5). The average heterozygosity among the population groups was approximately 70% with the overall extent of gene differentiation among the five groups being high (Gst = 0.046). Genetic affinity among the populations reveal very close association between the Kuki, Hmar, Naga, and Meitei. The Manipuri Muslims, despite being found in the same region, have had no admixture with these populations and maintain a substantial distance with the other groups. The genetic polymorphism data suggest that the studied systems can be used for human identity testing to estimate the frequency of a multiple locus STR DNA profile in population groups of northeastern India.

  9. Infrared fluorescent automated detection of thirteen short tandem repeat polymorphisms and one gender-determining system of the CODIS core system.

    PubMed

    Ricci, U; Sani, I; Guarducci, S; Biondi, C; Pelagatti, S; Lazzerini, V; Brusaferri, A; Lapini, M; Andreucci, E; Giunti, L; Giovannucci Uzielli, M L

    2000-11-01

    We used an infrared (IR) automated fluorescence monolaser sequencer for the analysis of 13 autosomal short tandem repeat (STR) systems (TPOX, D3S1358, FGA, CSF1PO, D5S818, D7S820, D8S1179, TH01, vWA, D13S317, D16S359, D18S51, D21S11) and the X-Y homologous gene amelogenin system. These two systems represent the core of the combined DNA index systems (CODIS). Four independent multiplex reactions, based on the polymerase chain reaction (PCR) technique and on the direct labeling of the forward primer of every primer pair, with a new molecule (IRDye800), were set up, permitting the exact characterization of the alleles by comparison with ladders of specific sequenced alleles. This is the first report of the whole analysis of the STRs of the CODIS core using an IR automated DNA sequencer. The protocol was used to solve paternity/maternity tests and for population studies. The electrophoretic system also proved useful for the correct typing of those loci differing in size by only 2 bp. A sensibility study demonstrated that the test can detect an average of 10 pg of undegraded human DNA. We also performed a preliminary study analyzing some forensic samples and mixed stains, which suggested the usefulness of using this analytical system for human identification as well as for forensic purposes.

  10. Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians.

    PubMed

    Budowle, B; Moretti, T R; Baumstark, A L; Defenbaugh, D A; Keys, K M

    1999-11-01

    Allele distributions for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Caucasian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p = 0.010, Bahamians); CSF1PO (p = 0.014, Trinidadians); TPOX (p = 0.011, Jamaicans and p = 0.035, U.S. Caucasians); and D16S539 (p = 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other comparable data within the same major population group.

  11. High throughput visualization and analysis of human short tandem repeat polymorphisms (STRP`s) using an infrared based automated DNA sequencer

    SciTech Connect

    Jang, G.Y.; Gartside, B.O.; Brumbaugh, J.A.

    1994-09-01

    Short tandem repeat polymorphisms (STRPs) including di-, tri-, and tetranucleotide repeats are very useful markers for gene mapping, genetic diagnosis, and forensics because they are highly polymorphic, abundant throughout the mammalian genome, and amplifiable by the polymerase chain reaction (PCR). In order to meet the demand for large scale gene mapping and genetic diagnosis, the overall speed of genotyping STRPs should be increased. Automated detection systems using laser irradiation along with infrared fluorescently labeled PCR primers or dATP`s have been used for improved detection of PCR amplified STRPs when compared to conventional radioactive detection methods. Here, we report protocols that provide high throughput visualization and analysis of PCR amplified STRPs using the LI-COR Model 4000S DNA Sequencer. Short (15 cm separation distance) gels were used which produced rapid migration of the DNA fragments to the scanning detector (less than 1 hour from sample loading to detection of up to 350 base long DNA fragments). Seven percent denaturing acrylamide gels with a constant 2000V were employed for fast and adequate resolution. A 64 well format was used for loading (60 samples with 4 lanes for standard markers). Multiple loading of samples (using the same gel up to 3 times) has been achieved. In addition, we have multiplexed more than one locus per lane. By applying these conditions (60 samples x 3 loci x loads/gel x 2 gels/day) it is possible to generate images for over 1000 person loci in less than a day. Images were analyzed using Scanalytics RFLPscan software. The output data gave each allele size in number of base pairs.

  12. Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping.

    PubMed

    Kim, Yong Tae; Lee, Dohwan; Heo, Hyun Young; Sim, Jeong Eun; Woo, Kwang Man; Kim, Do Hyun; Im, Sung Gap; Seo, Tae Seok

    2016-04-15

    A fully integrated slidable and valveless microsystem, which performs solid phase DNA extraction (SPE), micro-polymerase chain reaction (μPCR) and micro-capillary electrophoresis (μCE) coupled with a portable genetic analyser, has been developed for forensic genotyping. The use of a slidable chip, in which a 1 μL-volume of the PCR chamber was patterned at the center, does not necessitate any microvalves and tubing systems for fluidic control. The functional micro-units of SPE, μPCR, and μCE were fabricated on a single glass wafer by conventional photolithography, and the integrated microdevice consists of three layers: from top to bottom, a slidable chip, a channel wafer in which a SPE chamber, a mixing microchannel, and a CE microchannel were fabricated, and a Ti/Pt resistance temperature detector (RTD) wafer. The channel glass wafer and the RTD glass wafer were thermally bonded, and the slidable chip was placed on the designated functional unit. The entire process from the DNA extraction using whole human blood sample to identification of target Y chromosomal short tandem repeat (STR) loci was serially carried out with simply sliding the slidable chamber from one to another functional unit. Monoplex and multiplex detection of amelogenin and mini Y STR loci were successfully analysed on the integrated slidable SPE-μPCR-μCE microdevice by using 1 μL whole human blood within 60 min. The proposed advanced genetic analysis microsystem is capable of point-of-care DNA testing with sample-in-answer-out capability, more importantly, without use of complicated microvalves and microtubing systems for liquid transfer.

  13. Survey of the fragile X syndrome CGG repeat and the short-tandem-repeat and single-nucleotide-polymorphism haplotypes in an African American population.

    PubMed

    Crawford, D C; Schwartz, C E; Meadows, K L; Newman, J L; Taft, L F; Gunter, C; Brown, W T; Carpenter, N J; Howard-Peebles, P N; Monaghan, K G; Nolin, S L; Reiss, A L; Feldman, G L; Rohlfs, E M; Warren, S T; Sherman, S L

    2000-02-01

    Previous studies have shown that specific short-tandem-repeat (STR) and single-nucleotide-polymorphism (SNP)-based haplotypes within and among unaffected and fragile X white populations are found to be associated with specific CGG-repeat patterns. It has been hypothesized that these associations result from different mutational mechanisms, possibly influenced by the CGG structure and/or cis-acting factors. Alternatively, haplotype associations may result from the long mutational history of increasing instability. To understand the basis of the mutational process, we examined the CGG-repeat size, three flanking STR markers (DXS548-FRAXAC1-FRAXAC2), and one SNP (ATL1) spanning 150 kb around the CGG repeat in unaffected (n=637) and fragile X (n=63) African American populations and compared them with unaffected (n=721) and fragile X (n=102) white populations. Several important differences were found between the two ethnic groups. First, in contrast to that seen in the white population, no associations were observed among the African American intermediate or "predisposed" alleles (41-60 repeats). Second, two previously undescribed haplotypes accounted for the majority of the African American fragile X population. Third, a putative "protective" haplotype was not found among African Americans, whereas it was found among whites. Fourth, in contrast to that seen in whites, the SNP ATL1 was in linkage equilibrium among African Americans, and it did not add new information to the STR haplotypes. These data indicate that the STR- and SNP-based haplotype associations identified in whites probably reflect the mutational history of the expansion, rather than a mutational mechanism or pathway.

  14. Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations.

    PubMed

    Iacolina, L; Brajković, V; Canu, A; Šprem, N; Cubric-Curik, V; Fontanesi, L; Saarma, U; Apollonio, M; Scandura, M

    2016-12-01

    Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5-10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (HD  = 0.904 ± 0.011 and HD  = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (FST  = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.

  15. Comparison of southern Chinese Han and Brazilian Caucasian mutation rates at autosomal short tandem repeat loci used in human forensic genetics.

    PubMed

    Sun, Hongyu; Liu, Sujuan; Zhang, Yinming; Whittle, Martin R

    2014-01-01

    The short tandem repeat (STR) loci used in human genetic studies are characterized by having relatively high mutation rates. In particular, to ensure an appropriate evaluation of genetic evidence in parentage and forensic analyses, it is essential to have accurate estimates of the mutation rates associated with the commonly used autosomal and sex chromosome STR loci. Differences in STR mutation rates between different ethnic groups should also be determined. Mutation data from two laboratories working with different ethnic groups were extracted from many meiotic transmissions ascertained for 15 autosomal STR loci currently used in forensic routine. Forty-five thousand and eighty-five trios were checked for the biological consistency of maternity and paternity through the analysis of a minimum of 15 loci. Mutations were scored as paternal, maternal, or ambiguous according to the most parsimonious explanation for the inconsistency, using always the least requiring hypothesis in terms of number of repeat differences. The main findings are: (a) the overall mutation rate across the 15 loci was 9.78 × 10(-4) per gamete per generation (95% CI = 9.30 × 10(-4)-1.03 × 10(-3)), and with just 48 (out of 1,587) exceptions, all of the mutations were single-step; (b) repeat gains were more frequent than losses; (c) longer alleles were found to be more mutable; and (d) the mutation rates differ at some loci between the two ethnic groups. Large worldwide meiotic transmission datasets are still needed to measure allele-specific mutation rates at the STR loci consensually used in forensic genetics.

  16. Evidence for human meiotic recombination interference obtained through construction of a short tandem repeat-polymorphism linkage map of chromosome 19

    SciTech Connect

    Weber, J.L.; Wang, Z.; Hansen, K.; Stephenson, M.; Kappel, C.; Salzman, S.; Wilkie, P.J. ); Keats, B. ); Dracopoli, N.C. ); Brandriff, B.F.; Olsen, A.S. )

    1993-11-01

    An improved linkage map for human chromosome 19 containing 35 short tandem repeat polymorphisms (STRPs) and one VNTR (D19S20) was constructed. The map included 12 new (GATA)[sub n] tetranucleotide STRPs. Although total lengths of the male (114 cM) and female (128 cM) maps were similar, at both ends of the chromosome male recombination exceeded female recombination, while in the interior portion of the map female recombination was in excess. Cosmid clones containing the STRP sequences were identified and were positioned along the chromosome by fluorescent in situ hybridization. Four rounds of careful checking and removal of genotyping errors allowed biologically relevant conclusions to be made concerning the numbers and distributions of recombination events on chromosome 19. The average numbers of recombinations per chromosome matched closely the lengths of the genetic maps computed by using the program CRIMAP. Significant numbers of chromosomes with zero, one, two, or three recombinations were detected as products of both female and male meioses. On the basis of the total number of observed pairs of recombination events in which only a single informative marker was situated between the two recombinations, a maximal estimate for the rate of meiotic STRP [open quotes]gene[close quotes] conversion without recombination was calculated as 3 [times] 10[sup [minus]4]/meiosis. For distances up to 30 cM between recombinations, many fewer chromosomes which had undergone exactly two recombinations were observed than were expected on the basis of the assumption of independent recombination locations. This strong new evidence for human meiotic interference will help to improve the accuracy of interpretation of clinical DNA test results involving polymorphisms flanking a genetic abnormality. 61 refs., 2 figs., 5 tabs.

  17. Population Genetic Analysis of Haplotypes Based on 17 Short Tandem Repeat Loci on Y Chromosome in Population Sample from Eastern Croatia

    PubMed Central

    Gršković, Branka; Mršić, Gordan; Vrdoljak, Andro; Merkaš, Siniša; Anđelinović, Šimun

    2010-01-01

    Aim To investigate the population genetics of 17 short tandem repeat (STR) loci on the Y chromosome in the population of eastern Croatia. Methods We carried out a statistical analysis of the data from previously performed genetic analysis collected during routine forensic work by the Forensic Science Centre “Ivan Vučetić.” A total of 220 unrelated healthy men from eastern Croatia were selected for the purpose of this study. Genomic DNA was extracted by Chelex from FTA® cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y-chromosome haplotype reference database online analysis tool. Results A total of 207 haplotypes were recorded, 197 of which were unique (90%). Haplotype diversity was 0.9993, with the most frequent haplotype found in 4 of 220 men (1.8%). Average locus diversity was 0.600, and it ranged from 0.256 for DYS392 to 0.780 for DYS458. Our results were compared with the pattern of Y-chromosome variability in publicly available population samples based on a minimal European haplotype set of 9 STRs and the greatest resemblance was found with samples from the Croatian capital of Zagreb, from Bosnia and Herzegovina, and from Serbia. Conclusion This is the first description of Y chromosome haplotyping of the population of eastern Croatia, which may serve as a basis for genetic epidemiology and forensic studies. Further studies are needed for characterization of the genetic structure of the Y-chromosome in the modern Croatian population. PMID:20564762

  18. Separation of isomeric short-chain acyl-CoAs in plant matrices using ultra-performance liquid chromatography coupled with tandem mass spectrometry.

    PubMed

    Purves, Randy W; Ambrose, Stephen J; Clark, Shawn M; Stout, Jake M; Page, Jonathan E

    2015-02-01

    Acyl coenzyme A (acyl-CoA) thioesters are important intermediates in cellular metabolism and being able to distinguish among them is critical to fully understanding metabolic pathways in plants. Although significant advances have been made in the identification and quantification of acyl-CoAs using liquid chromatography tandem mass spectrometry (LC-MS/MS), separation of isomeric species such as isobutyryl- and n-butyrl-CoA has remained elusive. Here we report an ultra-performance liquid chromatography (UPLC)-MS/MS method for quantifying short-chain acyl-CoAs including isomeric species n-butyryl-CoA and isobutyryl-CoA as well as n-valeryl-CoA and isovaleryl-CoA. The method was applied to the analysis of extracts of hop (Humulus lupulus) and provided strong evidence for the existence of an additional structural isomer of valeryl-CoA, 2-methylbutyryl-CoA, as well as an unexpected isomer of hexanoyl-CoA. The results showed differences in the acyl-CoA composition among varieties of Humulus lupulus, both in glandular trichomes and cone tissues. When compared with the analysis of hemp (Cannabis sativa) extracts, the contribution of isobutyryl-CoAs in hop was greater as would be expected based on the downstream polyketide products. Surprisingly, branched chain valeryl-CoAs (isovaleryl-CoA and 2-methylbutyryl-CoA) were the dominant form of valeryl-CoAs in both hop and hemp. The capability to separate these isomeric forms will help to understand biochemical pathways leading to specialized metabolites in plants.

  19. Sibling assessment based on likelihood ratio and total number of shared alleles using 21 short tandem repeat loci included in the GlobalFiler™ kit.

    PubMed

    Inoue, Hiroyuki; Manabe, Sho; Fujii, Koji; Iwashima, Yasuki; Miyama, Saori; Tanaka, Ayako; Saitoh, Hisako; Iwase, Hirotaro; Tamaki, Keiji; Sekiguchi, Kazumasa

    2016-03-01

    Sibling assessment using the 15 autosomal short tandem repeat (STR) loci included in the Identifiler® kit can be difficult when comparing an unidentified party to an alleged sibling. Therefore, we investigated the likelihood ratio (LR) and the total number of shared alleles (TNSA) for sibship determination using the 21 autosomal STR loci included in the GlobalFiler™ kit. We computationally generated the genotypes of 10,000 sibling pairs and 10,000 unrelated pairs based on previously reported allele frequencies of the 15 Identifiler loci and the remaining 6 GlobalFiler loci. The LR and the TNSA were then calculated in each pair using the 15 and 21 loci. Next, these calculations were applied to 22 actual sibling pairs. LR values ⩾ 10,000 were observed in 48% of the sibling pairs using the 15 loci and in 80% of the sibling pairs using the 21 loci. The TNSA distribution between siblings and unrelated pairs was more divergent in GlobalFiler than in Identifiler. TNSA values ⩾ 20 were found only in true siblings in Identifiler, while TNSA values ⩾24 in GlobalFiler. In Identifiler, all pairs with TNSA ⩾ 24 had LR values ⩾ 10,000 and the same was true in GlobalFiler for TNSA ⩾29. Therefore, increasing the number of loci is very efficient for sibship determination. The LR is most reliable for determining sibship. However, TNSA values may be useful for the preliminary method of LR values because LR value demonstrated a significantly positive correlation with TNSA value in both Identifiler and GlobalFiler.

  20. The effect of single nucleotide polymorphisms in G-rich regions of high-risk human papillomaviruses on structural diversity of DNA.

    PubMed

    Marušič, Maja; Hošnjak, Lea; Krafčikova, Petra; Poljak, Mario; Viglasky, Viktor; Plavec, Janez

    2017-05-01

    Infection with high-risk human papillomaviruses (HPVs) can lead to development of cancer of the head and neck and anogenital regions. G-rich sequences found in genomes of high-risk HPVs can fold into non-canonical secondary structures that could serve as 3D motifs distinct from double-stranded DNA and present recognition sites for ligands and opportunity for gene expression modulation. Combination of UV, CD and NMR spectroscopy and PAGE electrophoresis were used as they offer complementary insights into structural changes of G-rich oligonucleotides. G-rich region of HPV16 is shown to preferentially form hairpin structures, while regions of HPV18, HPV52 and HPV58 fold into four-stranded DNA structures called G-quadruplexes. Single nucleotide polymorphisms found in G-rich sequences have been found to promote formation of hairpin structures of HPV16 and have affected number of species formed in G-rich region of HPV52, whereas they have exhibited minimal effect on the formation of HPV18 and HPV58 G-quadruplex structures. These structural changes were reflected in differences in apparent thermal stabilities. Potential of G-rich sequences as drug targets was evaluated based on the results of the current study. HPV16 and HPV18 are considered less appropriate targets due to several single nucleotide polymorphisms and low stability, respectively. On the other hand, HPV52 and HPV58 could be used for small-molecule mediated stabilization. G-rich sequences occurring in high-risk HPVs can fold into hairpin and G-quadruplex structures that could be potentially utilized as drug targets. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Multifunctional G-rich and RRM-containing domains of TbRGG2 perform separate yet essential functions in trypanosome RNA editing.

    PubMed

    Foda, Bardees M; Downey, Kurtis M; Fisk, John C; Read, Laurie K

    2012-09-01

    Efficient editing of Trypanosoma brucei mitochondrial RNAs involves the actions of multiple accessory factors. T. brucei RGG2 (TbRGG2) is an essential protein crucial for initiation and 3'-to-5' progression of editing. TbRGG2 comprises an N-terminal G-rich region containing GWG and RG repeats and a C-terminal RNA recognition motif (RRM)-containing domain. Here, we perform in vitro and in vivo separation-of-function studies to interrogate the mechanism of TbRGG2 action in RNA editing. TbRGG2 preferentially binds preedited mRNA in vitro with high affinity attributable to its G-rich region. RNA-annealing and -melting activities are separable, carried out primarily by the G-rich and RRM domains, respectively. In vivo, the G-rich domain partially complements TbRGG2 knockdown, but the RRM domain is also required. Notably, TbRGG2's RNA-melting activity is dispensable for RNA editing in vivo. Interactions between TbRGG2 and MRB1 complex proteins are mediated by both G-rich and RRM-containing domains, depending on the binding partner. Overall, our results are consistent with a model in which the high-affinity RNA binding and RNA-annealing activities of the G-rich domain are essential for RNA editing in vivo. The RRM domain may have key functions involving interactions with the MRB1 complex and/or regulation of the activities of the G-rich domain.

  2. Multifunctional G-Rich and RRM-Containing Domains of TbRGG2 Perform Separate yet Essential Functions in Trypanosome RNA Editing

    PubMed Central

    Foda, Bardees M.; Downey, Kurtis M.; Fisk, John C.

    2012-01-01

    Efficient editing of Trypanosoma brucei mitochondrial RNAs involves the actions of multiple accessory factors. T. brucei RGG2 (TbRGG2) is an essential protein crucial for initiation and 3′-to-5′ progression of editing. TbRGG2 comprises an N-terminal G-rich region containing GWG and RG repeats and a C-terminal RNA recognition motif (RRM)-containing domain. Here, we perform in vitro and in vivo separation-of-function studies to interrogate the mechanism of TbRGG2 action in RNA editing. TbRGG2 preferentially binds preedited mRNA in vitro with high affinity attributable to its G-rich region. RNA-annealing and -melting activities are separable, carried out primarily by the G-rich and RRM domains, respectively. In vivo, the G-rich domain partially complements TbRGG2 knockdown, but the RRM domain is also required. Notably, TbRGG2's RNA-melting activity is dispensable for RNA editing in vivo. Interactions between TbRGG2 and MRB1 complex proteins are mediated by both G-rich and RRM-containing domains, depending on the binding partner. Overall, our results are consistent with a model in which the high-affinity RNA binding and RNA-annealing activities of the G-rich domain are essential for RNA editing in vivo. The RRM domain may have key functions involving interactions with the MRB1 complex and/or regulation of the activities of the G-rich domain. PMID:22798390

  3. G-rich sequence-functionalized polystyrene microsphere-based instantaneous derivatization for the chemiluminescent amplified detection of DNA.

    PubMed

    Xin, Liang; Cao, Zhijuan; Lau, Choiwan; Kai, Masaaki; Lu, Jianzhong

    2010-01-01

    Herein, we develop a novel chemiluminescence (CL) approach with high sensitivity and excellent selectivity, by taking advantage of magnetic beads as preconcentration carriers and polystyrene microspheres as an amplification platform. Briefly, a 'sandwich-type' detection strategy is employed in our design, which involves capture probe DNA immobilized on the surface of carboxyl-terminated magnetic beads and multiple biotinylated reporter DNA self-assembled on the surface of streptavidin-modified polystyrene microspheres. The reporter DNA includes a guanine nucleobase-rich (G-rich) sequence domain for the generation of light and an additional tethered nucleic acid domain complementary with the target DNA. The CL signal is obtained via a novel instantaneous derivatization reaction between a specific CL reagent and the guanine nucleo-bases rich in the target and reporter DNA. As a result, we demonstrate that this DNA assay is reproducible, stable, easy to use, and can sensitively detect femtomolar target DNA related to anthrax lethal factors with excellent differentiation ability for single-base mismatched sequences. Overall, this new CL protocol couples the high sensitivity of CL analysis with effective magnetic separation for discriminating against unwanted constituents such as mismatched sequences, and hence, offers great promise for DNA hybridization analysis. Copyright (c) 2009 John Wiley & Sons, Ltd.

  4. QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences

    PubMed Central

    Menendez, Camille; Frees, Scott; Bagga, Paramjeet S.

    2012-01-01

    Naturally occurring G-quadruplex structural motifs, formed by guanine-rich nucleic acids, have been reported in telomeric, promoter and transcribed regions of mammalian genomes. G-quadruplex structures have received significant attention because of growing evidence for their role in important biological processes, human disease and as therapeutic targets. Lately, there has been much interest in the potential roles of RNA G-quadruplexes as cis-regulatory elements of post-transcriptional gene expression. Large-scale computational genomics studies on G-quadruplexes have difficulty validating their predictions without laborious testing in ‘wet’ labs. We have developed a bioinformatics tool, QGRS-H Predictor that can map and analyze conserved putative Quadruplex forming 'G'-Rich Sequences (QGRS) in mRNAs, ncRNAs and other nucleotide sequences, e.g. promoter, telomeric and gene flanking regions. Identifying conserved regulatory motifs helps validate computations and enhances accuracy of predictions. The QGRS-H Predictor is particularly useful for mapping homologous G-quadruplex forming sequences as cis-regulatory elements in the context of 5′- and 3′-untranslated regions, and CDS sections of aligned mRNA sequences. QGRS-H Predictor features highly interactive graphic representation of the data. It is a unique and user-friendly application that provides many options for defining and studying G-quadruplexes. The QGRS-H Predictor can be freely accessed at: http://quadruplex.ramapo.edu/qgrs/app/start. PMID:22576365

  5. Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms

    PubMed Central

    Vermeulen, Mark; Wollstein, Andreas; van der Gaag, Kristiaan; Lao, Oscar; Xue, Yali; Wang, Qiuju; Roewer, Lutz; Knoblauch, Hans; Tyler-Smith, Chris; de Knijff, Peter; Kayser, Manfred

    2012-01-01

    We analysed 67 short tandem repeat polymorphisms from the non-recombining part of the Y-chromosome (Y-STRs), including 49 rarely-studied simple single-copy (ss)Y-STRs and 18 widely-used Y-STRs, in 590 males from 51 populations belonging to 8 worldwide regions (HGDP-CEPH panel). Although autosomal DNA profiling provided no evidence for close relationship, we found 18 Y-STR haplotypes (defined by 67 Y-STRs) that were shared by two to five men in 13 worldwide populations, revealing high and widespread levels of cryptic male relatedness. Maximal (95.9%) haplotype resolution was achieved with the best 25 out of 67 Y-STRs in the global dataset, and with the best 3-16 markers in regional datasets (89.6-100% resolution). From the 49 rarely-studied ssY-STRs, the 25 most informative markers were sufficient to reach the highest possible male lineage differentiation in the global (92.2% resolution), and 3-15 markers in the regional datasets (85.4-100%). Considerably lower haplotype resolutions were obtained with the three commonly-used Y-STR sets (Minimal Haplotype, PowerPlex Y®, and AmpFlSTR® Yfiler®). Six ssY-STRs (DYS481, DYS533, DYS549, DYS570, DYS576 and DYS643) were most informative to supplement the existing Y-STR kits for increasing haplotype resolution, or – together with additional ssY-STRs - as a new set for maximizing male lineage differentiation. Mutation rates of the 49 ssY-STRs were estimated from 403 meiotic transfers in deep-rooted pedigrees, and ranged from ~4.8×10−4 for 31 ssY-STRs with no mutations observed to 1.3×10−2 and 1.5×10−2 for DYS570 and DYS576, respectively, the latter representing the highest mutation rates reported for human Y-STRs so far. Our findings thus demonstrate that ssY-STRs are useful for maximizing global and regional resolution of male lineages, either as a new set, or when added to commonly-used Y-STR sets, and support their application to forensic, genealogical and anthropological studies. PMID:19647704

  6. Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens.

    PubMed

    Just, Rebecca S; Moreno, Lilliana I; Smerick, Jill B; Irwin, Jodi A

    2017-05-01

    Though the utility of next-generation sequencing (NGS) technologies for forensic short tandem repeat (STR) typing has been evident for several years, commercially available assays and software solutions developed specifically to meet forensic needs have only recently become available. One of these, the ForenSeq™ DNA Signature Prep Kit (Illumina, Inc.) sequences 27 autosomal STR (aSTR) and 24 Y chromosome STR (Y-STR) loci (concurrent with additional nuclear markers) per multiplexed sample, with automated secondary and tertiary analyses of the data accomplished via the associated ForenSeq™ Universal Analysis Software (UAS). In this study we investigated the performance of the ForenSeq system for aSTR and Y-STR typing by examination of 151 sample libraries developed from high quality DNAs amplified at the target 1ng template. Utilizing PCR Primer Mix B, greater than 99.5% of aSTR loci and 97.0% of Y-STR loci were recovered when 42 or fewer sample libraries were pooled for sequencing. A direct comparison of UAS developed fragment length results to capillary electrophoresis (CE) based data identified only two allele call discrepancies when no UAS quality flag was triggered. Review of the ForenSeq data indicated that most samples with total sequence read counts exceeding 40,000 could be interpreted to develop nearly complete aSTR genotypes or Y-STR haplotypes. However, markers D22S1045 and DYS392 produced poor or inconsistent results even when sample read counts were greater than 85,000. Excluding these two loci, analyst-interpreted aSTR and Y-STR ForenSeq profiles were 99.96% and 100% concordant, respectively, with CE data. In addition to demonstrating concordance on par with other CE kit to kit comparisons, the results from this study will assist laboratories seeking to develop workflows for high volume processing and analysis of aSTRs and Y-STRs from reference-type specimens using the ForenSeq system. Copyright © 2017 The Authors. Published by Elsevier B.V. All

  7. Y-chromosome short tandem repeat intermediate variant alleles DYS392.2, DYS449.2, and DYS385.2 delineate new phylogenetic substructure in human Y-chromosome haplogroup tree.

    PubMed

    Myres, Natalie M; Ritchie, Kathleen H; Lin, Alice A; Hughes, Robert H; Woodward, Scott R; Underhill, Peter A

    2009-06-01

    To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree. Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles. We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently. Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context.

  8. Y-chromosome Short Tandem Repeat Intermediate Variant Alleles DYS392.2, DYS449.2, and DYS385.2 Delineate New Phylogenetic Substructure in Human Y-chromosome Haplogroup Tree

    PubMed Central

    Myres, Natalie M.; Ritchie, Kathleen H.; Lin, Alice A.; Hughes, Robert H.; Woodward, Scott R.; Underhill, Peter A.

    2009-01-01

    Aim To determine the human Y-chromosome haplogroup backgrounds of intermediate-sized variant alleles displayed by short tandem repeat (STR) loci DYS392, DYS449, and DYS385, and to evaluate the potential of each intermediate variant to elucidate new phylogenetic substructure within the human Y-chromosome haplogroup tree. Methods Molecular characterization of lineages was achieved using a combination of Y-chromosome haplogroup defining binary polymorphisms and up to 37 short tandem repeat loci. DNA sequencing and median-joining network analyses were used to evaluate Y-chromosome lineages displaying intermediate variant alleles. Results We show that DYS392.2 occurs on a single haplogroup background, specifically I1*-M253, and likely represents a new phylogenetic subdivision in this European haplogroup. Intermediate variants DYS449.2 and DYS385.2 both occur on multiple haplogroup backgrounds, and when evaluated within specific haplogroup contexts, delineate new phylogenetic substructure, with DYS449.2 being informative within haplogroup A-P97 and DYS385.2 in haplogroups D-M145, E1b1a-M2, and R1b*-M343. Sequence analysis of variant alleles observed within the various haplogroup backgrounds showed that the nature of the intermediate variant differed, confirming the mutations arose independently. Conclusions Y-chromosome short tandem repeat intermediate variant alleles, while relatively rare, typically occur on multiple haplogroup backgrounds. This distribution indicates that such mutations arise at a rate generally intermediate to those of binary markers and Y-STR loci. As a result, intermediate-sized Y-STR variants can reveal phylogenetic substructure within the Y-chromosome phylogeny not currently detected by either binary or Y-STR markers alone, but only when such variants are evaluated within a haplogroup context. PMID:19480020

  9. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province.

    PubMed

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  10. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province

    PubMed Central

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  11. Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA.

    PubMed

    Zhang, Jia-yu; Zheng, Ke-wei; Xiao, Shan; Hao, Yu-hua; Tan, Zheng

    2014-01-29

    We recently reported that a DNA:RNA hybrid G-quadruplex (HQ) forms during transcription of DNA that bears two or more tandem guanine tracts (G-tract) on the nontemplate strand. Putative HQ-forming sequences are enriched in the nearby 1000 nt region right downstream of transcription start sites in the nontemplate strand of warm-blooded animals, and HQ regulates transcription under both in vitro and in vivo conditions. Therefore, knowledge of the mechanism of HQ formation is important for understanding the biological function of HQ as well as for manipulating gene expression by targeting HQ. In this work, we studied the mechanism of HQ formation using an in vitro T7 transcription model. We show that RNA synthesis initially produces an R-loop, a DNA:RNA heteroduplex formed by a nascent RNA transcript and the template DNA strand. In the following round of transcription, the RNA in the R-loop is displaced, releasing the RNA in single-stranded form (ssRNA). Then the G-tracts in the RNA can jointly form HQ with those in the nontemplate DNA strand. We demonstrate that the structural cascade R-loop → ssRNA → HQ offers opportunities to intercept HQ formation, which may provide a potential method to manipulate gene expression.

  12. Tandem electroabsorption modulators integrated with DFB laser by ultra-low-pressure selective-area-growth MOCVD for 10 GHz optical short pulse generation

    NASA Astrophysics Data System (ADS)

    Zhao, Q.; Pan, J. Q.; Zhang, J.; Zhou, G. T.; Wu, J.; Wang, L. F.; Wang, W.

    2005-08-01

    A novel device of tandem MQW EAMs monolithically integrated with a DFB laser is fabricated by an ultra-low-pressure (22 mbar) selective area growth MOCVD technique. Experimental results exhibit superior device characteristics with low threshold of 19 mA, output light power of 4.5 mW, and over 20 dB extinction ratio when coupled to a single mode fibre. Moreover, over 10 GHz modulation bandwidth is developed with a driving voltage of 2 V. Using this sinusoidal voltage driven integrated device, 10 GHz repetition rate pulse with an actual width of 13.7 ps without any compression elements is obtained.

  13. Tandem electro-absorption modulators integrated with DFB laser by ultra-low-pressure selective-area-growth MOCVD for 10 GHz optical short-pulse generation

    NASA Astrophysics Data System (ADS)

    Zhao, Q.; Pan, J. Q.; Zhang, J.; Zhou, G. T.; Wu, J.; Wang, L. F.; Wang, W.

    2005-11-01

    A novel device of tandem multiple quantum wells (MQWs) electroabsorption modulators (EAMs) monolithically integrated with DFB laser is fabricated by ultra-low-pressure (22 mbar) selective area growth (SAG) MOCVD technique. Experimental results exhibit superior device characteristics with low threshold of 19 mA, output light power of 4.5 mW, and over 20 dB extinction ratio when coupled into a single mode fiber. Moreover, over 10 GHz modulation bandwidth is developed with a driving voltage of 2 V. Using this sinusoidal voltage driven integrated device, 10GHz repetition rate pulse with a width of 13.7 ps without any compression elements is obtained.

  14. High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research

    PubMed Central

    Reichwald, Kathrin; Lauber, Chris; Nanda, Indrajit; Kirschner, Jeanette; Hartmann, Nils; Schories, Susanne; Gausmann, Ulrike; Taudien, Stefan; Schilhabel, Markus B; Szafranski, Karol; Glöckner, Gernot; Schmid, Michael; Cellerino, Alessandro; Schartl, Manfred; Englert, Christoph; Platzer, Matthias

    2009-01-01

    Background The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research. Results To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred. Conclusions Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri. PMID:19210790

  15. High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research.

    PubMed

    Reichwald, Kathrin; Lauber, Chris; Nanda, Indrajit; Kirschner, Jeanette; Hartmann, Nils; Schories, Susanne; Gausmann, Ulrike; Taudien, Stefan; Schilhabel, Markus B; Szafranski, Karol; Glöckner, Gernot; Schmid, Michael; Cellerino, Alessandro; Schartl, Manfred; Englert, Christoph; Platzer, Matthias

    2009-02-11

    The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research. To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred. Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri.

  16. [Conformational polymorphysm of G-rich fragments of DNA Alu-repeats. II. the putative role of G-quadruplex structures in genomic rearrangements].

    PubMed

    Varizhuk, A M; Sekridova, A V; Tankevich, M V; Podgorsky, V S; Smirnov, I P; Pozmogova, G E

    2016-11-01

    Three evolutionary conserved sites of Alu repeats (PQS2, PQS3 and PQS4) were shown to form stable inter- and intramolecular G-quadruplexes (GQs) in vitro. Structures and topologies of these GQs were elucidated using spectral methods. Self-association of G-rich Alu fragments was studied. Dimeric GQ formation from two distal identical or different putative quadruplex sites - (PQS2)2, (PQS3)2 or PQS2-PQS3 - within one lengthy DNA strand was demonstrated by a FRET-based method. Oligomer PQS4 (folded into a parallel intramolecular GQ) was shown to form stacks of quadruplexes that are stabilized by stacking interactions of external G-tetrads (this was confirmed by DOSY NMR, AFM microscopy and differential CD spectroscopy). Comparative analysis of the properties of various GQs allowed us to put forward a hypothesis of two general mechanisms of intermolecular GQ-dependant genomic rearrangements: 1) formation of a dimeric GQs; 2) association of pre-folded intramolecular parallel GQs from different strands into GQ-stacks. Thus, the observed co-localization of G-rich motifs of Alu elements with double-strand break hotspots and rearrangement hotspots may be accounted for by the specific secondary structure of these motifs. At the same time, this is likely primarily due to high abundance of such G-rich Alu fragments in the genome.

  17. G-quadruplex and G-rich sequence stimulate Pif1p-catalyzed downstream duplex DNA unwinding through reducing waiting time at ss/dsDNA junction.

    PubMed

    Zhang, Bo; Wu, Wen-Qiang; Liu, Na-Nv; Duan, Xiao-Lei; Li, Ming; Dou, Shuo-Xing; Hou, Xi-Miao; Xi, Xu-Guang

    2016-09-30

    Alternative DNA structures that deviate from B-form double-stranded DNA such as G-quadruplex (G4) DNA can be formed by G-rich sequences that are widely distributed throughout the human genome. We have previously shown that Pif1p not only unfolds G4, but also unwinds the downstream duplex DNA in a G4-stimulated manner. In the present study, we further characterized the G4-stimulated duplex DNA unwinding phenomenon by means of single-molecule fluorescence resonance energy transfer. It was found that Pif1p did not unwind the partial duplex DNA immediately after unfolding the upstream G4 structure, but rather, it would dwell at the ss/dsDNA junction with a 'waiting time'. Further studies revealed that the waiting time was in fact related to a protein dimerization process that was sensitive to ssDNA sequence and would become rapid if the sequence is G-rich. Furthermore, we identified that the G-rich sequence, as the G4 structure, equally stimulates duplex DNA unwinding. The present work sheds new light on the molecular mechanism by which G4-unwinding helicase Pif1p resolves physiological G4/duplex DNA structures in cells.

  18. G-quadruplex and G-rich sequence stimulate Pif1p-catalyzed downstream duplex DNA unwinding through reducing waiting time at ss/dsDNA junction

    PubMed Central

    Zhang, Bo; Wu, Wen-Qiang; Liu, Na-Nv; Duan, Xiao-Lei; Li, Ming; Dou, Shuo-Xing; Hou, Xi-Miao; Xi, Xu-Guang

    2016-01-01

    Alternative DNA structures that deviate from B-form double-stranded DNA such as G-quadruplex (G4) DNA can be formed by G-rich sequences that are widely distributed throughout the human genome. We have previously shown that Pif1p not only unfolds G4, but also unwinds the downstream duplex DNA in a G4-stimulated manner. In the present study, we further characterized the G4-stimulated duplex DNA unwinding phenomenon by means of single-molecule fluorescence resonance energy transfer. It was found that Pif1p did not unwind the partial duplex DNA immediately after unfolding the upstream G4 structure, but rather, it would dwell at the ss/dsDNA junction with a ‘waiting time’. Further studies revealed that the waiting time was in fact related to a protein dimerization process that was sensitive to ssDNA sequence and would become rapid if the sequence is G-rich. Furthermore, we identified that the G-rich sequence, as the G4 structure, equally stimulates duplex DNA unwinding. The present work sheds new light on the molecular mechanism by which G4-unwinding helicase Pif1p resolves physiological G4/duplex DNA structures in cells. PMID:27471032

  19. Rapid diagnosis of aneuploidy in chromosomes 13, 18, 21, X and Y by quantitative fluorescence-PCR combined with short tandem repeat and fluorescence-labeled homologous gene quantitative‑PCR using 4-color fluorescently labeled universal primers.

    PubMed

    Long, Ju; Ye, Xuehe; Weng, Xunjin; Fu, Kepeng; Sun, Lei; Pang, Wanrong

    2013-11-01

    The present study aimed to develop a rapid diagnostic test of aneuploidy in chromosomes 13, 18, 21, X and Y through a program combining short tandem repeat (STR) typing with fluorescence-labeled homologous gene quantitative‑polymerase chain reaction (fHGQ-PCR), which avoids misjudgment risks by using one method alone. Furthermore, fluorescently labeled universal primers not only ensure the accuracy of the results but also reduces the cost of fluorescent labels. The verification of DNA extracted from samples confirmed by karyotype analysis with quantitative fluorescence (QF)-PCR shows that the results obtained using the QF-PCR program are consistent with the results of karyotype analysis in rapidly diagnosing the aneuploidy of chromosomes 13, 18, 21, X and Y.

  20. Tandem betatron

    DOEpatents

    Keinigs, Rhonald K.

    1992-01-01

    Two betatrons are provided in tandem for alternately accelerating an electron beam to avoid the single flux swing limitation of conventional betatrons and to accelerate the electron beam to high energies. The electron beam is accelerated in a first betatron during a period of increasing magnetic flux. The eletron beam is extracted from the first betatron as a peak magnetic flux is reached and then injected into a second betatron at a time of minimum magnetic flux in the second betatron. The cycle may be repeated until the desired electron beam energy is obtained. In one embodiment, the second betatron is axially offset from the first betatron to provide for electron beam injection directly at the axial location of the beam orbit in the second betatron.

  1. G-rich DNA-induced stress response blocks type-I-IFN but not CXCL10 secretion in monocytes

    PubMed Central

    Herzner, Anna-Maria; Wolter, Steven; Zillinger, Thomas; Schmitz, Saskia; Barchet, Winfried; Hartmann, Gunther; Bartok, Eva; Schlee, Martin

    2016-01-01

    Excessive inflammation can cause damage to host cells and tissues. Thus, the secretion of inflammatory cytokines is tightly regulated at transcriptional, post-transcriptional and post-translational levels and influenced by cellular stress responses, such as endoplasmic reticulum (ER) stress or apoptosis. Here, we describe a novel type of post-transcriptional regulation of the type-I-IFN response that was induced in monocytes by cytosolic transfection of a short immunomodulatory DNA (imDNA), a G-tetrad forming CpG-free derivative of the TLR9 agonist ODN2216. When co-transfected with cytosolic nucleic acid stimuli (DNA or 3P-dsRNA), imDNA induced caspase-3 activation, translational shutdown and upregulation of stress-induced genes. This stress response inhibited the type-I-IFN induction at the translational level. By contrast, the induction of most type-I-IFN-associated chemokines, including Chemokine (C-X-C Motif) Ligand (CXCL)10 was not affected, suggesting a differential translational regulation of chemokines and type-I-IFN. Pan-caspase inhibitors could restore IFN-β secretion, yet, strikingly, caspase inhibition did not restore global translation but instead induced a compensatory increase in the transcription of IFN-β but not CXCL10. Altogether, our data provide evidence for a differential regulation of cytokine release at both transcriptional and post-transcriptional levels which suppresses type-I-IFN induction yet allows for CXCL10 secretion during imDNA-induced cellular stress. PMID:27941826

  2. A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage.

    PubMed

    Xue, Zhihong; Hennelly, Scott; Doyle, Boryana; Gulati, Arune A; Novikova, Irina V; Sanbonmatsu, Karissa Y; Boyer, Laurie A

    2016-10-06

    Long non-coding RNAs (lncRNAs) are an emerging class of transcripts that can modulate gene expression; however, their mechanisms of action remain poorly understood. Here, we experimentally determine the secondary structure of Braveheart (Bvht) using chemical probing methods and show that this ∼590 nt transcript has a modular fold. Using CRISPR/Cas9-mediated editing of mouse embryonic stem cells, we find that deletion of 11 nt in a 5' asymmetric G-rich internal loop (AGIL) of Bvht (bvht(dAGIL)) dramatically impairs cardiomyocyte differentiation. We demonstrate a specific interaction between AGIL and cellular nucleic acid binding protein (CNBP/ZNF9), a zinc-finger protein known to bind single-stranded G-rich sequences. We further show that CNBP deletion partially rescues the bvht(dAGIL) mutant phenotype by restoring differentiation capacity. Together, our work shows that Bvht functions with CNBP through a well-defined RNA motif to regulate cardiovascular lineage commitment, opening the door for exploring broader roles of RNA structure in development and disease.

  3. Strong transcription blockage mediated by R-loop formation within a G-rich homopurine–homopyrimidine sequence localized in the vicinity of the promoter

    PubMed Central

    Soo Shin, Jane Hae

    2017-01-01

    Abstract Guanine-rich (G-rich) homopurine–homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA–DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA–DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription ‘bursting’) and may also have practical implications for the design of expression vectors. PMID:28498974

  4. Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs.

    PubMed

    Abdelmohsen, Kotb; Tominaga, Kumiko; Lee, Eun Kyung; Srikantan, Subramanya; Kang, Min-Ju; Kim, Mihee M; Selimyan, Roza; Martindale, Jennifer L; Yang, Xiaoling; Carrier, France; Zhan, Ming; Becker, Kevin G; Gorospe, Myriam

    2011-10-01

    RNA-binding proteins (RBPs) regulate gene expression at many post-transcriptional levels, including mRNA stability and translation. The RBP nucleolin, with four RNA-recognition motifs, has been implicated in cell proliferation, carcinogenesis and viral infection. However, the subset of nucleolin target mRNAs and the influence of nucleolin on their expression had not been studied at a transcriptome-wide level. Here, we globally identified nucleolin target transcripts, many of which encoded cell growth- and cancer-related proteins, and used them to find a signature motif on nucleolin target mRNAs. Surprisingly, this motif was very rich in G residues and was not only found in the 3'-untranslated region (UTR), but also in the coding region (CR) and 5'-UTR. Nucleolin enhanced the translation of mRNAs bearing the G-rich motif, since silencing nucleolin did not change target mRNA stability, but decreased the size of polysomes forming on target transcripts and lowered the abundance of the encoded proteins. In summary, nucleolin binds G-rich sequences in the CR and UTRs of target mRNAs, many of which encode cancer proteins, and enhances their translation.

  5. Stereoselective synthesis of eight-membered cyclic ethers by tandem Nicholas reaction/ring-closing metathesis: a short synthesis of (+)-cis-Lauthisan.

    PubMed

    Ortega, Nuria; Martín, Tomás; Martín, Víctor S

    2006-03-02

    Cis-2,8-disubstituted oxocanes and the parent unsaturated precursors were prepared from the corresponding Co2(CO)6-cycloalkynic ethers. Key steps in such synthesis were the ether linkage formation by intermolecular Nicholas reaction, RCM of the suitable acyclic dienyl ether and montmorillonite K-10 induced isomerization of the complexed cycloalkyne. A short synthesis of (+)-cis-lauthisan taking advantage of the developed methodology is described.

  6. In situ detection of tandem DNA repeat length

    SciTech Connect

    Yaar, R.; Szafranski, P.; Cantor, C.R.; Smith, C.L.

    1996-11-01

    A simple method for scoring short tandem DNA repeats is presented. An oligonucleotide target, containing tandem repeats embedded in a unique sequence, was hybridized to a set of complementary probes, containing tandem repeats of known lengths. Single-stranded loop structures formed on duplexes containing a mismatched (different) number of tandem repeats. No loop structure formed on duplexes containing a matched (identical) number of tandem repeats. The matched and mismatched loop structures were enzymatically distinguished and differentially labeled by treatment with S1 nuclease and the Klenow fragment of DNA polymerase. 7 refs., 4 figs.

  7. Ancestry of the Brazilian TP53 c.1010G>A (p.Arg337His, R337H) Founder Mutation: Clues from Haplotyping of Short Tandem Repeats on Chromosome 17p

    PubMed Central

    Paskulin, Diego Davila; Giacomazzi, Juliana; Achatz, Maria Isabel; Costa, Sandra; Reis, Rui Manoel; Hainaut, Pierre; dos Santos, Sidney Emanuel Batista; Ashton-Prolla, Patricia

    2015-01-01

    Rare germline mutations in TP53 (17p13.1) cause a highly penetrant predisposition to a specific spectrum of early cancers, defining the Li-Fraumeni Syndrome (LFS). A germline mutation at codon 337 (p.Arg337His, c1010G>A) is found in about 0.3% of the population of Southern Brazil. This mutation is associated with partially penetrant LFS traits and is found in the germline of patients with early cancers of the LFS spectrum unselected for familial history. To characterize the extended haplotypes carrying the mutation, we have genotyped 9 short tandem repeats on chromosome 17p in 12 trios of Brazilian p.Arg337His carriers. Results confirm that all share a common ancestor haplotype of Caucasian/Portuguese-Iberic origin, distant in about 72–84 generations (2000 years assuming a 25 years intergenerational distance) and thus pre-dating European migration to Brazil. So far, the founder p.Arg337His haplotype has not been detected outside Brazil, with the exception of two residents of Portugal, one of them of Brazilian origin. On the other hand, increased meiotic recombination in p.Arg337His carriers may account for higher than expected haplotype diversity. Further studies comparing haplotypes in populations of Brazil and of other areas of Portuguese migration are needed to understand the historical context of this mutation in Brazil. PMID:26618902

  8. Ancestry of the Brazilian TP53 c.1010G>A (p.Arg337His, R337H) Founder Mutation: Clues from Haplotyping of Short Tandem Repeats on Chromosome 17p.

    PubMed

    Paskulin, Diego Davila; Giacomazzi, Juliana; Achatz, Maria Isabel; Costa, Sandra; Reis, Rui Manoel; Hainaut, Pierre; dos Santos, Sidney Emanuel Batista; Ashton-Prolla, Patricia

    2015-01-01

    Rare germline mutations in TP53 (17p13.1) cause a highly penetrant predisposition to a specific spectrum of early cancers, defining the Li-Fraumeni Syndrome (LFS). A germline mutation at codon 337 (p.Arg337His, c1010G>A) is found in about 0.3% of the population of Southern Brazil. This mutation is associated with partially penetrant LFS traits and is found in the germline of patients with early cancers of the LFS spectrum unselected for familial history. To characterize the extended haplotypes carrying the mutation, we have genotyped 9 short tandem repeats on chromosome 17p in 12 trios of Brazilian p.Arg337His carriers. Results confirm that all share a common ancestor haplotype of Caucasian/Portuguese-Iberic origin, distant in about 72-84 generations (2000 years assuming a 25 years intergenerational distance) and thus pre-dating European migration to Brazil. So far, the founder p.Arg337His haplotype has not been detected outside Brazil, with the exception of two residents of Portugal, one of them of Brazilian origin. On the other hand, increased meiotic recombination in p.Arg337His carriers may account for higher than expected haplotype diversity. Further studies comparing haplotypes in populations of Brazil and of other areas of Portuguese migration are needed to understand the historical context of this mutation in Brazil.

  9. Highly efficient nuclear DNA typing of the World War II skeletal remains using three new autosomal short tandem repeat amplification kits with the extended European Standard Set of loci.

    PubMed

    Zupanic Pajnic, Irena; Gornjak Pogorelc, Barbara; Balazic, Joze; Zupanc, Tomaz; Stefanic, Borut

    2012-02-15

    To perform an efficiency study of three new amplification kits with the extended European Standard Set (ESS) of loci for autosomal short tandem repeat (STR) typing of skeletal remains excavated from the World War II mass graves in Slovenia. In the beginning of the 2011, we analyzed 102 bones and teeth using the PowerPlex ESX 17 System (Promega), AmpFiSTR NGM PCR Amplification Kit (Applied Biosystems), and Investigator ESSplex Kit (Qiagen). We cleaned the bones and teeth, removed surface contamination, and ground them into a powder using liquid nitrogen. Prior to DNA isolation with Biorobot EZ1 (Qiagen), 0.5 g bone or tooth powder was decalcified. Nuclear DNA of the samples was quantified using real-time polymerase chain reaction. All three kits used the same extract with the amplification conditions recommended by the manufacturers. We extracted up to 131 ng DNA/g of powder from the bones and teeth. All three amplification kits showed very similar efficiency, since DNA typing was successful with all amplification kits in 101 out of 102 bones and teeth, which represents a 99% success rate. The commercially available ESX 17, ESSplex, and NGM kits are highly reliable for STR typing of World War II skeletal remains with the DNA extraction method optimized in our laboratory.

  10. Short-chain peptides identification of scorpion Buthus martensi Karsch venom by employing high orthogonal 2D-HPLC system and tandem mass spectrometry.

    PubMed

    Xu, Junyan; Zhang, Xiuli; Guo, Zhimou; Yan, Jingyu; Yu, Long; Li, Xiuling; Xue, Xingya; Liang, Xinmiao

    2012-10-01

    Scorpion venom contains a considerable variety of neurotoxic peptides that can act on ionic channels. Here, we describe an orthogonal 2D-reversed phase/hydrophilic interaction chromatography system (RPLC/HILIC) and use it to separate short-chain peptides from Asian scorpion Buthus martensi Karsch (BmK) venom in a high throughput format. Due to its high orthogonality and efficiency, 18 homogenous peptides were purified and sequence identified by MS/MS with collision-induced dissociation. Among them, four peptides were discovered, which only have evidence at transcript-level, were first purified from crude venom in this study. Two peptides named BmKK2-b and Martentoxin-b were found the new cleaved chains of known BmKK2 and Martentoxin. In addition, two novel peptides named BmKK12 and BmKK16 in this paper were sequenced by de novo MS/MS, which we predict, are members of potassium channel toxin α-KTx 17 subfamily by homology to other known peptides found in the Swiss-Prot protein database.

  11. Fingerprint enhancement revisited and the effects of blood enhancement chemicals on subsequent profiler Plus fluorescent short tandem repeat DNA analysis of fresh and aged bloody fingerprints.

    PubMed

    Frégeau, C J; Germain, O; Fourney, R M

    2000-03-01

    This study was aimed at determining the effect of seven blood enhancement reagents on the subsequent Profiler Plus fluorescent STR DNA analysis of fresh or aged bloody fingerprints deposited on various porous and nonporous surfaces. Amido Black, Crowle's Double Stain. 1,8-diazafluoren-9-one (DFO), Hungarian Red, leucomalachite green, luminol and ninhydrin were tested on linoleum, glass, metal, wood (pine, painted white), clothing (85% polyester/15% cotton, 65% polyester/35% cotton, and blue denim) and paper (Scott 2-ply and Xerox-grade). Preliminary experiments were designed to determine the optimal blood dilutions to use to ensure a DNA typing result following chemical enhancement. A 1:200 blood dilution deposited on linoleum and enhanced with Crowle's Double Stain generated enough DNA for one to two rounds of Profiler Plus PCR amplification. A comparative study of the DNA yields before and after treatment indicated that the quantity of DNA recovered from bloody fingerprints following enhancement was reduced by a factor of 2 to 12. Such a reduction in the DNA yields could potentially compromise DNA typing analysis in the case of small stains. The blood enhancement chemicals selected were also evaluated for their capability to reveal bloodmarks on the various porous and nonporous surfaces chosen in this study. Luminol. Amido Black and Crowle's Double Stain showed the highest sensitivity of all seven chemicals tested and revealed highly diluted (1:200) bloody fingerprints. Both luminol and Amido Black produced excellent results on both porous and nonporous surfaces, but Crowle's Double Stain failed to produce any results on porous substrates. Hungarian Red, DFO, leucomalachite green and ninhydrin showed lower sensitivities. Enhancement of bloodmarks using any of the chemicals selected, and short-term exposure to these same chemicals (i.e., less than 54 days), had no adverse effects on the PCR amplification of the nine STR systems surveyed (D3S 1358, HumvWA, Hum

  12. Comprehensive profiling of mercapturic acid metabolites from dietary acrylamide as short-term exposure biomarkers for evaluation of toxicokinetics in rats and daily internal exposure in humans using isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry.

    PubMed

    Zhang, Yu; Wang, Qiao; Cheng, Jun; Zhang, Jingshun; Xu, Jiaojiao; Ren, Yiping

    2015-09-24

    Mercapturic acid metabolites from dietary acrylamide are important short-term exposure biomarkers for evaluating the in vivo toxicity of acrylamide. Most of studies have focused on the measurement of two metabolites, N-acetyl-S-(2-carbamoylethyl)-L-cysteine (AAMA) and N-acetyl-S-(2-carbamoyl-2-hydroxyethyl)-L-cysteine (GAMA). Thus, the comprehensive profile of acrylamide urinary metabolites cannot be fully understood. We developed an isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for the simultaneous determination of all four mercapturic acid adducts of acrylamide and its primary metabolite glycidamide under the electroscopy ionization negative (ESI-) mode in the present study. The limit of detection (LOD) and limit of quantification (LOQ) of the analytes ranged 0.1-0.3 ng/mL and 0.4-1.0 ng/mL, respectively. The recovery rates with low, intermediate and high spiking levels were calculated as 95.5%-105.4%, 98.2%-114.0% and 92.2%-108.9%, respectively. Acceptable within-laboratory reproducibility (RSD<7.0%) substantially supported the use of current method for robust analysis. Rapid pretreatment procedures and short run time (8 min per sample) ensured good efficiency of metabolism profiling, indicating a wide application for investigating short-term internal exposure of dietary acrylamide. Our proposed UHPLC-MS/MS method was successfully applied to the toxicokinetic study of acrylamide in rats. Meanwhile, results of human urine analysis indicated that the levels of N-acetyl-S-(2-carbamoylethyl)-L-cysteine-sulfoxide (AAMA-sul), which did not appear in the mercapturic acid metabolites in rodents, were more than the sum of GAMA and N-acetyl-S-(1-carbamoyl-2-hydroxyethyl)-L-cysteine (iso-GAMA). Thus, AAMA-sul may alternatively become a specific biomarker for investigating the acrylamide exposure in humans. Current proposed method provides a substantial methodology support for comprehensive profiling of

  13. Asymmetric tandem organic solar cells

    NASA Astrophysics Data System (ADS)

    Howells, Thomas J.

    where it is used to predict the short-circuit current (Jsc) generation of the sub-cells, which is not accessible experimentally. Current-matching is then used to predict the Jsc of the complete tandem device. . As a support to the optical modelling, ellipsometry measurements of thin films of ClAlPc are presented. These films of known thickness are analysed to extract the complex refractive index for use in optical modelling calculations. A dependence of the complex refractive index on film thickness and substrate is also noted. Finally, the external quantum efficiency (EQE) technique is considered as applied to solar cells, and an additional method is proposed to characterise current balancing in asymmetric tandem cells under illumination. This technique is verified experimentally by two separate sets of data..

  14. 4.5S RNA is encoded by hundreds of tandemly linked genes, has a short half-life, and is hydrogen bonded in vivo to poly(A)-terminated RNAs in the cytoplasm of cultured mouse cells.

    PubMed Central

    Schoeniger, L O; Jelinek, W R

    1986-01-01

    4.5S RNA is a group of RNAs 90 to 94 nucleotides long (length polymorphism due to a varying number of UMP residues at the 3' end) that form hydrogen bonds with poly(A)-terminated RNAs isolated from mouse, hamster, or rat cells (W. R. Jelinek and L. Leinwand, Cell 15:205-214, 1978; F. Harada, N. Kato, and H.-O. Hoshino, Nucleic Acids Res. 7:909-917, 1979). We have cloned a gene that encodes the 4.5S RNA. It is repeated 850 (sigma = 54) times per haploid mouse genome and 690 (sigma = 59) times per haploid rat genome. Most, if not all, of the repeats in both species are arrayed in tandem. The repeat unit is 4,245 base pairs long in mouse DNA (the complete base sequence of one repeat unit is presented) and approximately 5,300 base pairs in rat DNA. This accounts for approximately 3 X 10(6) base pairs of genomic DNA in each species, or 0.1% of the genome. Cultured murine erythroleukemia cells contain 13,000 molecules per cell of the 4.5S RNA, which can be labeled to equilibrium in 90 min by [3H]uridine added to the culture medium. The 4.5S RNA, therefore, has a short half-life. The 4.5S RNA can be cross-linked in vivo by 4'-aminomethyl-4,5',8-trimethylpsoralen to murine erythroleukemia cell poly(A)-terminated cytoplasmic RNA contained in ribonucleoprotein particles. Images PMID:2431280

  15. Effect of the Capsicoside G-rich Fraction from Pepper (Capsicum annuum L.) Seeds on High-fat Diet-induced Obesity in Mice.

    PubMed

    Sung, Jeehye; Jeong, Heon Sang; Lee, Junsoo

    2016-11-01

    Obesity is one of the most common metabolic syndromes and is a major threat to human health worldwide. Given the size of this problem, there is growing interest in natural agents that may decrease obesity. In this study, we investigated the anti-obesity effect of a capsicoside G-rich fraction (CRF; 13.35% capsicoside G) isolated from pepper seeds in diet-induced obese mice. C57BL/6J mice were fed either a normal diet or a high-fat diet (HFD), with or without CRF (HFD + CRF; 10 and 100 mg/kg body weight). The body weight and food efficiency ratio of mice fed HFD + CRF were lower in comparison to that of mice fed only an HFD. Epididymal adipose tissue weight and adipocyte hypertrophy were significantly lower in HFD + CRF mice than in HFD mice. The fat deposition in the liver of mice fed HFD + CRF was lower compared to that of mice fed only an HFD. CRF significantly reversed the HFD-induced elevation of the expression of key adipocyte differentiation regulators, including peroxisome proliferator-activated receptor γ, CCAAT/enhancer-binding protein α, sterol regulatory element binding protein 1c, and their target genes. These results suggest that CRF could be used as dietary therapy for the prevention of obesity and obesity-related metabolic diseases. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  16. The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation.

    PubMed

    Benhalevy, Daniel; Gupta, Sanjay K; Danan, Charles H; Ghosal, Suman; Sun, Hong-Wei; Kazemier, Hinke G; Paeschke, Katrin; Hafner, Markus; Juranek, Stefan A

    2017-03-21

    The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs. CNBP preferentially bound G-rich elements in the target mRNA coding sequences, most of which were previously found to form G-quadruplex and other stable structures in vitro. Functional analyses, including RNA sequencing, ribosome profiling, and quantitative mass spectrometry, revealed that CNBP binding did not influence target mRNA abundance but rather increased their translational efficiency. Considering that CNBP binding prevented G-quadruplex structure formation in vitro, we hypothesize that CNBP is supporting translation by resolving stable structures on mRNAs.

  17. Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA

    PubMed Central

    Munroe, Stephen H.; Morales, Christopher H.; Duyck, Tessa H.; Waters, Paul D.

    2015-01-01

    The α-thyroid hormone receptor gene (TRα) codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3’ end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30) located downstream of the alternative 3’splice site of TRα2 mRNA and antisense to the 3’UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing. PMID:26368571

  18. DNA-methyltransferase1 (DNMT1) binding to CpG rich GABAergic and BDNF promoters is increased in the brain of schizophrenia and bipolar disorder patients.

    PubMed

    Dong, E; Ruzicka, W B; Grayson, D R; Guidotti, A

    2015-09-01

    The down regulation of glutamic acid decarboxylase67 (GAD1), reelin (RELN), and BDNF expression in brain of schizophrenia (SZ) and bipolar (BP) disorder patients is associated with overexpression of DNA methyltransferase1 (DNMT1) and ten-eleven translocase methylcytosine dioxygenase1 (TET1). DNMT1 and TET1 belong to families of enzymes that methylate and hydroxymethylate cytosines located proximal to and within cytosine phosphodiester guanine (CpG) islands of many gene promoters, respectively. Altered promoter methylation may be one mechanism underlying the down-regulation of GABAergic and glutamatergic gene expression. However, recent reports suggest that both DNMT1 and TET1 directly bind to unmethylated CpG rich promoters through their respective Zinc Finger (ZF-CXXC) domains. We report here, that the binding of DNMT1 to GABAergic (GAD1, RELN) and glutamatergic (BDNF-IX) promoters is increased in SZ and BP disorder patients and this increase does not necessarily correlate with enrichment in promoter methylation. The increased DNMT1 binding to these promoter regions is detected in the cortex but not in the cerebellum of SZ and BP disorder patients, suggesting a brain region and neuron specific dependent mechanism. Increased binding of DNMT1 positively correlates with increased expression of DNMT1 and with increased binding of MBD2. In contrast, the binding of TET1 to RELN, GAD1 and BDNF-IX promoters failed to change. These data are consistent with the hypothesis that the down-regulation of specific GABAergic and glutamatergic genes in SZ and BP disorder patients may be mediated, at least in part, by a brain region specific and neuronal-activity dependent DNMT1 action that is likely independent of its DNA methylation activity.

  19. Feeding microalgae meal (All-G Rich; CCAP 4087/2) to beef heifers. I: Effects on longissimus lumborum steak color and palatibility.

    PubMed

    Phelps, K J; Drouillard, J S; O'Quinn, T G; Burnett, D D; Blackmon, T L; Axman, J E; Van Bibber-Krueger, C L; Gonzalez, J M

    2016-09-01

    The objective of this study was to examine effects of 4 levels of microalgae meal (All-G Rich, CCAP 4087/2; Alltech Inc., Nicholasville, KY) supplementation to the diet of finishing heifers on longissimus lumborum (LL) steak PUFA content, beef palatability, and color stability. Crossbred heifers ( = 288; 452 ± 23 kg initial BW) were allocated to pens (36 pens and 8 heifers/pen), stratified by initial pen BW (3,612 ± 177 kg), and randomly assigned within strata to 1 of 4 treatments: 0, 50, 100, and 150 g·heifer·d of microalgae meal. After 89 d of feeding, cattle were harvested and LL were collected for determination of fatty acid composition and Warner-Bratzler shear force (WBSF), trained sensory panel evaluation, and 7-d retail color stability and lipid oxidation analyses. Feeding microalgae meal to heifers increased (quadratic, < 0.01) the content of 22:6-3 and increased (linear, < 0.01) the content of 20:5-3. Feeding increasing levels of microalgae meal did not impact total SFA or MUFA ( > 0.25) but tended ( = 0.10) to increase total PUFA in a quadratic manner ( = 0.03). Total omega-6 PUFA decreased (linear, = 0.01) and total omega-3 PUFA increased (quadratic, < 0.01) as microalgae meal level increased in the diet, which caused a decrease (quadratic, < 0.01) in the omega-6:omega-3 fatty acid ratio. Feeding microalgae meal did not affect WBSF values or sensory panel evaluation of tenderness, juiciness, or beef flavor scores ( > 0.16); however, off-flavor intensity increased with increasing concentration of microalgae meal in the diet (quadratic, < 0.01). From d 5 through 7 of retail display, steaks from heifers fed microalgae meal had a reduced a* value and oxymyoglobin surface percentage, with simultaneous increased surface metmyoglobin formation (quadratic, < 0.01). Lipid oxidation analysis indicated that at d 0 and 7 of display, as the concentration of microalgae meal increased in the diet, the level of oxidation increased (quadratic, < 0.01). Muscle fiber

  20. Feeding microalgae meal (All-G Rich; CCAP 4067/2) to beef heifers. II: Effects on ground beef color and palatability.

    PubMed

    Phelps, K J; Drouillard, J S; O'Quinn, T G; Burnett, D D; Blackmon, T L; Axman, J E; Van Bibber-Krueger, C L; Gonzalez, J M

    2016-09-01

    The objective of this study was to examine the effects of feeding microalgae meal (All-G Rich, CCAP 4087/2; Alltech Inc., Nicholasville, KY) to finishing heifers on 85% lean and 15% fat (85/15) ground beef PUFA content, palatability, and color stability. Crossbred heifers ( = 288; 452 ± 23 kg initial BW) were allocated to pens (36 pens and 8 heifers/pen), stratified by initial pen BW (3,612 ± 177 kg), and randomly assigned within strata to 1 of 4 treatments: 0, 50, 100, and 150 g·heifer·d of microalgae meal. After 89 d of feeding, a subset of heifers (3/pen) was harvested and the rectus femoris, vastus lateralis, vastus medialis, and vastus intermedius were collected for processing into ground beef. At 42 d postmortem, 85/15 ground beef was formulated and formed into 112-g patties and fatty acid composition, subjective palatability, and 96-h retail color stability analyses were conducted. Increasing dietary microalgae meal concentration increased ground beef 20:5-3 and 22:6-3 fatty acids (quadratic, < 0.01). There was a treatment × hour interaction for all color attributes ( < 0.01). On d 0, microalgae tended ( = 0.08) to decrease L*, but patties had similar L* values the remainder of display ( > 0.12). Feeding microalgae meal affected ( = 0.02) b* at 24 h and decreased (linear, = 0.08) b* at 48 h. From h 0 to 36 of display, microalgae affected redness of patties ( < 0.02), and from 48 to 72 h, microalgae meal decreased a* value (linear, < 0.04). Microalgae meal did not impact sensory panel firmness, overall tenderness, or juiciness scores ( > 0.20) but tended to affect ( = 0.10) cohesiveness scores. As the amount of microalgae meal fed to heifers increased, beef flavor intensity decreased (linear, < 0.01) and off-flavor intensity increased (quadratic, < 0.05). Surface oxymyoglobin and metmyoglobin were impacted by microalgae meal from 12 to 36 h of display ( < 0.01). From 48 to 84 h of display, feeding microalgae meal to heifers decreased (linear, < 0

  1. Tandem mobile robot system

    DOEpatents

    Buttz, James H.; Shirey, David L.; Hayward, David R.

    2003-01-01

    A robotic vehicle system for terrain navigation mobility provides a way to climb stairs, cross crevices, and navigate across difficult terrain by coupling two or more mobile robots with a coupling device and controlling the robots cooperatively in tandem.

  2. Monolithic Parallel Tandem Organic Photovoltaic Cell with Transparent Carbon Nanotube Interlayer

    NASA Technical Reports Server (NTRS)

    Tanaka, S.; Mielczarek, K.; Ovalle-Robles, R.; Wang, B.; Hsu, D.; Zakhidov, A. A.

    2009-01-01

    We demonstrate an organic photovoltaic cell with a monolithic tandem structure in parallel connection. Transparent multiwalled carbon nanotube sheets are used as an interlayer anode electrode for this parallel tandem. The characteristics of front and back cells are measured independently. The short circuit current density of the parallel tandem cell is larger than the currents of each individual cell. The wavelength dependence of photocurrent for the parallel tandem cell shows the superposition spectrum of the two spectral sensitivities of the front and back cells. The monolithic three-electrode photovoltaic cell indeed operates as a parallel tandem with improved efficiency.

  3. Monolithic Parallel Tandem Organic Photovoltaic Cell with Transparent Carbon Nanotube Interlayer

    NASA Technical Reports Server (NTRS)

    Tanaka, S.; Mielczarek, K.; Ovalle-Robles, R.; Wang, B.; Hsu, D.; Zakhidov, A. A.

    2009-01-01

    We demonstrate an organic photovoltaic cell with a monolithic tandem structure in parallel connection. Transparent multiwalled carbon nanotube sheets are used as an interlayer anode electrode for this parallel tandem. The characteristics of front and back cells are measured independently. The short circuit current density of the parallel tandem cell is larger than the currents of each individual cell. The wavelength dependence of photocurrent for the parallel tandem cell shows the superposition spectrum of the two spectral sensitivities of the front and back cells. The monolithic three-electrode photovoltaic cell indeed operates as a parallel tandem with improved efficiency.

  4. Advances in Tandem Mirror fusion power reactors

    SciTech Connect

    Perkins, L.J.; Logan, B.G.

    1986-05-20

    The Tandem Mirror exhibits several distinctive features which make the reactor embodiment of the principle very attractive: Simple low-technology linear central cell; steady-state operation; high-..beta.. operation; no driven current or disruptions; divertorless operation; direction conversion of end-loss power; low-surface heat loads; and advanced fusion fuel capability. In this paper, we examine these features in connection with two tandem mirror reactor designs, MARS and MINIMARS, and several advanced reactor concepts including the wall-stabilized reactor and the field-reversed mirror. With a novel compact end plug scheme employing octopole stabilization, MINIMARS is expressly designed for short construction times, factory-built modules, and a small (600 MWe) but economic reactor size. We have also configured the design for low radioactive afterheat and inherent/passive safety under LOCA/LOFA conditions, thereby obviating the need for expensive engineered safety systems. In contrast to the complex and expensive double-quadrupole end-cell of the MARS reactor, the compact octopole end-cell of MINIMARS enables ignition to be achieved with much shorter central cell lengths and considerably improves the economy of scale for small (approx.250 to 600 MWe) tandem mirror reactors. Finally, we examine the prospects for realizing the ultimate potential of the tandem mirror with regard to both innovative configurations and novel neutron energy conversion schemes, and stress that advanced fuel applications could exploit its unique reactor features.

  5. Tandem Air Propellers

    NASA Technical Reports Server (NTRS)

    Lesley, E.P.

    1937-01-01

    Tests of 2-blade, adjustable-pitch, counterrotating tandem model propellers, adjusted to absorb equal power at maximum efficiency, were made at Stanford University. The characteristics, for 15 degrees, 25 degrees, 35 degrees, and 45 degrees pitch settings at 0.75 R of the forward propeller and for 8 1/2%, 15% and 30% diameter spacings, were compared with those of 2-blade and 4-blade propellers of the same blade form. The tests showed that the efficiency of the tandem propellers was from 0.5% to 4% greater than that of a 4-blade propeller and, at the high pitch settings, not appreciable inferior to that of a 2-blade propeller. It was found that the rear tandem propeller should be set at a pitch angle slightly less than that of the forward propeller to realize the condition of equal power at maximum efficiency. Under this condition the total power absorbed by the tandem propellers was from 3% to 9% more than that absorbed by the 4-blade propeller and about twice that absorbed by a 2-blade propeller.

  6. Solar-to-Chemical Energy Conversion with Photoelectrochemical Tandem Cells.

    PubMed

    Sivula, Kevin

    2013-01-01

    Efficiently and inexpensively converting solar energy into chemical fuels is an important goal towards a sustainable energy economy. An integrated tandem cell approach could reasonably convert over 20% of the sun's energy directly into chemical fuels like H2 via water splitting. Many different systems have been investigated using various combinations of photovoltaic cells and photoelectrodes, but in order to be economically competitive with the production of H2 from fossil fuels, a practical water splitting tandem cell must optimize cost, longevity and performance. In this short review, the practical aspects of solar fuel production are considered from the perspective of a semiconductor-based tandem cell and the latest advances with a very promising technology - metal oxide photoelectrochemical tandem cells - are presented.

  7. Tandem resonator reflectance modulator

    DOEpatents

    Fritz, I.J.; Wendt, J.R.

    1994-09-06

    A wide band optical modulator is grown on a substrate as tandem Fabry-Perot resonators including three mirrors spaced by two cavities. The absorption of one cavity is changed relative to the absorption of the other cavity by an applied electric field, to cause a change in total reflected light, as light reflecting from the outer mirrors is in phase and light reflecting from the inner mirror is out of phase with light from the outer mirrors. 8 figs.

  8. Tandem resonator reflectance modulator

    DOEpatents

    Fritz, Ian J.; Wendt, Joel R.

    1994-01-01

    A wide band optical modulator is grown on a substrate as tandem Fabry-Perot resonators including three mirrors spaced by two cavities. The absorption of one cavity is changed relative to the absorption of the other cavity by an applied electric field, to cause a change in total reflected light, as light reflecting from the outer mirrors is in phase and light reflecting from the inner mirror is out of phase with light from the outer mirrors.

  9. Bifacial tandem solar cells

    DOEpatents

    Wojtczuk, Steven J.; Chiu, Philip T.; Zhang, Xuebing; Gagnon, Edward; Timmons, Michael

    2016-06-14

    A method of fabricating on a semiconductor substrate bifacial tandem solar cells with semiconductor subcells having a lower bandgap than the substrate bandgap on one side of the substrate and with subcells having a higher bandgap than the substrate on the other including, first, growing a lower bandgap subcell on one substrate side that uses only the same periodic table group V material in the dislocation-reducing grading layers and bottom subcells as is present in the substrate and after the initial growth is complete and then flipping the substrate and growing the higher bandgap subcells on the opposite substrate side which can be of different group V material.

  10. Monolithic tandem solar cell

    DOEpatents

    Wanlass, Mark W.

    1991-01-01

    A single-crystal, monolithic, tandem, photovoltaic solar cell is described which includes (a) an InP substrate having upper and lower surfaces, (b) a first photoactive subcell on the upper surface of the InP substrate, and (c) a second photoactive subcell on the first subcell. The first photoactive subcell is GaInAsP of defined composition. The second subcell is InP. The two subcells are lattice matched. The solar cell can be provided as a two-terminal device or a three-terminal device.

  11. Negative tandem mirror

    SciTech Connect

    Poulsen, P.; Allen, S.L.; Casper, T.A.; Grubb, D.P.; Jong, R.A.; Nexsen, W.E.; Porter, G.D.; Simonen, T.C.

    1981-11-30

    A tandem mirror configuration can be created by combining hot electron end cell plasmas with neutral beam pumping. A region of large negative potential formed in each end cell confines electrons in the central cell. The requirement of charge neutrality causes the central cell potential to become negative with respect to ground in order to confine ions as well as electrons. We discuss the method of producing and calculating the desired axial potential profile, and show the calculated axial potential profile and plasma parameters for a negative configuration of TMX-Upgrade.

  12. Flute waves in a tandem mirror

    SciTech Connect

    Mikhailovskaya, L.V.

    1984-03-01

    Stability conditions are derived for flute waves in a short tandem mirror stabilized by end cells with a min B. The frequency spectrum of the flute waves is analyzed. Those conditions under which the resonant excitation of waves by ions and electrons must be taken into account are found. When end cells without a min B are added to a central mirror system, the system becomes destabilized as the result of resonant excitation of waves at a frequency near the precession frequency of ions having a finite energy distribution.

  13. Tandems as injectors for synchrotrons

    SciTech Connect

    Ruggiero, A.G.

    1992-08-01

    This is a review on the use of Tandem electrostatic accelerators for injection and filling of synchrotrons to accelerate intense beams of heavy-ions to relativistic energies. The paper emphasizes the need of operating the Tandems in pulsed mode for this application. It has been experimentally demonstrated that at the present this type of accelerators still provides the most reliable and best performance.

  14. A robust and cost-effective integrated process for nitrogen and bio-refractory organics removal from landfill leachate via short-cut nitrification, anaerobic ammonium oxidation in tandem with electrochemical oxidation.

    PubMed

    Wu, Li-Na; Liang, Da-Wei; Xu, Ying-Ying; Liu, Ting; Peng, Yong-Zhen; Zhang, Jie

    2016-07-01

    A cost-effective process, consisting of a denitrifying upflow anaerobic sludge blanket (UASB), an oxygen-limited anoxic/aerobic (A/O) process for short-cut nitrification, and an anaerobic reactor (ANR) for anaerobic ammonia oxidation (anammox), followed by an electrochemical oxidation process with a Ti-based SnO2-Sb2O5 anode, was developed to remove organics and nitrogen in a sewage diluted leachate. The final chemical oxygen demand (COD), ammonia nitrogen (NH4(+)-N) and total nitrogen (TN) of 70, 11.3 and 39 (all in mg/L), respectively, were obtained. TN removal in UASB, A/O and ANR were 24.6%, 49.6% and 16.1%, respectively. According to the water quality and molecular biology analysis, a high degree of anammox besides short-cut nitrification and denitrification occurred in A/O. Counting for 16.1% of TN removal in ANR, at least 43.2-49% of TN was removed via anammox. The anammox bacteria in A/O and ANR, were in respective titers of (2.5-5.9)×10(9) and 2.01×10(10)copy numbers/(gSS). Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Modern tandem control systems

    NASA Astrophysics Data System (ADS)

    Lutz, J. R.; Marsaudon, J. C.

    1993-04-01

    Nowadays, tandem electrostatic accelerators can benefit greatly from the growing possibilities provided by modern control facilities. Controlling an electrostatic accelerator first requires the solution of technological problems raised by the necessity of fitting inside the tank equipment which is highly stressed by the physical environment. Then, these controls can take advantage of new techniques which appear on the market. Present computer technology provides cheap powerful workstations for efficient operator interfacing, and new modular and distributed control concepts have been developed for general use in experimental physics, in data acquisition and in control systems. The general trend towards standardization is now accepted for both hardware and software and this brings benefits to the designer and the user.

  16. Covalently linked tandem lesions in DNA.

    PubMed

    Patrzyc, Helen B; Dawidzik, Jean B; Budzinski, Edwin E; Freund, Harold G; Wilton, John H; Box, Harold C

    2012-12-01

    Reactive oxygen species (ROS) generate a type of DNA damage called tandem lesions, two adjacent nucleotides both modified. A subcategory of tandem lesions consists of adjacent nucleotides linked by a covalent bond. Covalently linked tandem lesions generate highly characteristic liquid chromotography-tandem mass spectrometry (LC-MS/MS) elution profiles. We have used this property to comprehensively survey X-irradiated DNA for covalently linked tandem lesions. A total of 15 tandem lesions were detected in DNA irradiated in deoxygenated aqueous solution, five tandem lesions were detected in DNA that was irradiated in oxygenated solution.

  17. Covalently Linked Tandem Lesions in DNA

    PubMed Central

    Patrzyc, Helen B.; Dawidzik, Jean B.; Budzinski, Edwin E.; Freund, Harold G.; Wilton, John H.; Box, Harold C.

    2013-01-01

    Reactive oxygen species (ROS) generate a type of DNA damage called tandem lesions, two adjacent nucleotides both modified. A subcategory of tandem lesions consists of adjacent nucleotides linked by a covalent bond. Covalently linked tandem lesions generate highly characteristic liquid chromotography-tandem mass spectrometry (LC-MS/MS) elution profiles. We have used this property to comprehensively survey X-irradiated DNA for covalently linked tandem lesions. A total of 15 tandem lesions were detected in DNA irradiated in deoxygenated aqueous solution, five tandem lesions were detected in DNA that was irradiated in oxygenated solution. PMID:23106212

  18. Sequence alignment with tandem duplication

    SciTech Connect

    Benson, G.

    1997-12-01

    Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked farily well, it has long been apparent that other mutational events occur. In this paper, we introduce a new model, the DSI model which includes another common mutational event, tandem duplication. Tandem duplication produces tandem repeats which are common in DNA, making up perhaps 10% of the human genome. They are responsible for some human diseases and may serve a multitude of functions in DNA regulation and evolution. Using the DSI model, we develop new exact and heuristic algorithms for comparing and aligning DNA sequences when they contain tandem repeats. 30 refs., 3 figs.

  19. The design and numerical analysis of tandem thermophotovoltaic cells

    NASA Astrophysics Data System (ADS)

    Yang, Hao-Yu; Liu, Ren-Jun; Wang, Lian-Kai; Lü, You; Li, Tian-Tian; Li, Guo-Xing; Zhang, Yuan-Tao; Zhang, Bao-Lin

    2013-10-01

    In this paper, numerical analysis of GaSb =(Eg = 0.72 eV)/Ga0.84In0.16As0.14Sb0.86 (Eg = 0.53 eV) tandem thermophotovoltaic (TPV) cells is carried out by using Silvaco/Atlas software. In the tandem cells, a GaSb p-n homojunction is used for the top cell and a GaInAsSb p-n homojunction for the bottom cell. A heavily doped GaSb tunnel junction connects the two sub-cells together. The simulations are carried out at a radiator temperature of 2000 K and a cell temperature of 300 K. The radiation photons are injected from the top of the tandem cells. Key properties of the single- and dual-junction TPV cells, including I-V characteristic, maximum output power (Pmax), open-circuit voltage (Voc), short-circuit current (Isc), etc. are presented. The effects of the sub-cell thickness and carrier concentration on the key properties of tandem cells are investigated. A comparison of the dual-TPV cells with GaSb and GaInAsSb single junction cells shows that the Pmax of tandem cells is almost twice as great as that of the single-junction cells.

  20. Tandem Terminal Ion Source

    SciTech Connect

    2000-10-23

    OAK-B135 Tandem Terminal Ion Source. The terminal ion source (TIS) was used in several experiments during this reporting period, all for the {sup 7}Be({gamma}){sup 8}B experiment. Most of the runs used {sup 1}H{sup +} at terminal voltages from 0.3 MV to 1.5 MV. One of the runs used {sup 2}H{sup +} at terminal voltage of 1.4 MV. The other run used {sup 4}He{sup +} at a terminal voltage of 1.37 MV. The list of experiments run with the TIS to date is given in table 1 below. The tank was opened four times for unscheduled source repairs. On one occasion the tank was opened to replace the einzel lens power supply which had failed. The 10 kV unit was replaced with a 15 kV unit. The second time the tank was opened to repair the extractor supply which was damaged by a tank spark. On the next occasion the tank was opened to replace a source canal which had sputtered away. Finally, the tank was opened to replace the discharge bottle which had been coated with aluminum sputtered from the exit canal.

  1. Tandem Cylinder Noise Predictions

    NASA Technical Reports Server (NTRS)

    Lockhard, David P.; Khorrami, Mehdi R.; CHoudhari, Meelan M.; Hutcheson, Florence V.; Brooks, Thomas F.; Stead, Daniel J.

    2007-01-01

    In an effort to better understand landing-gear noise sources, we have been examining a simplified configuration that still maintains some of the salient features of landing-gear flow fields. In particular, tandem cylinders have been studied because they model a variety of component level interactions. The present effort is directed at the case of two identical cylinders spatially separated in the streamwise direction by 3.7 diameters. Experimental measurements from the Basic Aerodynamic Research Tunnel (BART) and Quiet Flow Facility (QFF) at NASA Langley Research Center (LaRC) have provided steady surface pressures, detailed off-surface measurements of the flow field using Particle Image Velocimetry (PIV), hot-wire measurements in the wake of the rear cylinder, unsteady surface pressure data, and the radiated noise. The experiments were conducted at a Reynolds number of 166 105 based on the cylinder diameter. A trip was used on the upstream cylinder to insure a fully turbulent shedding process and simulate the effects of a high Reynolds number flow. The parallel computational effort uses the three-dimensional Navier-Stokes solver CFL3D with a hybrid, zonal turbulence model that turns off the turbulence production term everywhere except in a narrow ring surrounding solid surfaces. The current calculations further explore the influence of the grid resolution and spanwise extent on the flow and associated radiated noise. Extensive comparisons with the experimental data are used to assess the ability of the computations to simulate the details of the flow. The results show that the pressure fluctuations on the upstream cylinder, caused by vortex shedding, are smaller than those generated on the downstream cylinder by wake interaction. Consequently, the downstream cylinder dominates the noise radiation, producing an overall directivity pattern that is similar to that of an isolated cylinder. Only calculations based on the full length of the model span were able to

  2. Tandem clerking: maximising workplace learning.

    PubMed

    Ahearn, David; Eccles, Jennifer; Jorna, Thomas; Kotecha, Ashish; Baker, Paul; Singh, Salil

    2013-12-01

    Medical assessment units (MAUs) are a valuable source of educational opportunities, but these are often not realised because of service pressures. We trialled a method of collaborative working, where junior and senior trainees work in 'tandem' to see new admissions. The roles are alternated throughout the shift with the aim of encouraging shared decisions, learning and feedback. A 4-month trial of tandem clerking was implemented. An anonymous questionnaire of junior doctors collected quantitative and qualitative data to assess educational aspects of tandem clerking in the MAU of a busy district general hospital. Junior doctors (n = 14) report seeing a larger number and wider variety of patients using tandem clerking, with more useful feedback and a greater chance of meeting learning objectives and completing assessments. Some respondents expressed concern over a lack of autonomy. Respondents stated they were less likely to spend time completing mundane and non-educational tasks. Eight respondents preferred the new system, four favoured the traditional system and two had no preference. Tandem clerking is an innovative method to increase the educational aspects of the assessment unit, both in terms of feedback opportunities and exposure to a wider variety of patients. The technique is partly dependent on the enthusiasm and interest of both parties. © 2013 John Wiley & Sons Ltd.

  3. MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services

    PubMed Central

    Pratt, Brian; Howbert, J. Jeffry; Tasman, Natalie I.; Nilsson, Erik J.

    2012-01-01

    Summary: MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows. Availability and implementation: MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL. Contact: brian.pratt@insilicos.com PMID:22072385

  4. MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.

    PubMed

    Pratt, Brian; Howbert, J Jeffry; Tasman, Natalie I; Nilsson, Erik J

    2012-01-01

    MR-Tandem adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem runs on any Hadoop cluster but offers special support for Amazon Web Services for creating inexpensive on-demand Hadoop clusters, enabling search volumes that might not otherwise be feasible with the compute resources a researcher has at hand. MR-Tandem is designed to drop in wherever X!Tandem is already in use and requires no modification to existing X!Tandem parameter files, and only minimal modification to X!Tandem-based workflows. MR-Tandem is implemented as a lightly modified X!Tandem C++ executable and a Python script that drives Hadoop clusters including Amazon Web Services (AWS) Elastic Map Reduce (EMR), using the modified X!Tandem program as a Hadoop Streaming mapper and reducer. The modified X!Tandem C++ source code is Artistic licensed, supports pluggable scoring, and is available as part of the Sashimi project at http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/xtandem/. The MR-Tandem Python script is Apache licensed and available as part of the Insilicos Cloud Army project at http://ica.svn.sourceforge.net/viewvc/ica/trunk/mr-tandem/. Full documentation and a windows installer that configures MR-Tandem, Python and all necessary packages are available at this same URL. brian.pratt@insilicos.com

  5. A nanocomposite interconnecting layer for tandem small molecular organic photovoltaic cells

    NASA Astrophysics Data System (ADS)

    Luo, D. Y.; Yu, L. M.; Man, J. X.; Liu, Z.; Lu, Z. H.

    2014-03-01

    A nanocomposite interconnecting layer of C60:LiF/Ag/MoOx had been applied in the tandem structure of organic photovoltaic cells to achieve high short circuit current (Jsc) and power conversion efficiency (PCE). The Jsc had been enhanced 40% after applying the nanocomposite interconnecting layer into a tandem structure compared to the conventional interconnecting layer of Bathocuproine (BCP)/Ag/MoOx. The improvement is due to the enhancement of the light absorption of the devices. A tandem device PCE of 3.04% was achieved by further improving the light absorption in the individual subcell units in the tandem structure by means of a bi-functional buffer layer of C60:LiF/BCP.

  6. Tandem-structured, hot electron based photovoltaic cell with double Schottky barriers.

    PubMed

    Lee, Young Keun; Lee, Hyosun; Park, Jeong Young

    2014-04-03

    We demonstrate a tandem-structured, hot electron based photovoltaic cell with double Schottky barriers. The tandem-structured, hot electron based photovoltaic cell is composed of two metal/semiconductor interfaces. Two types of tandem cells were fabricated using TiO2/Au/Si and TiO2/Au/TiO2, and photocurrent enhancement was detected. The double Schottky barriers lead to an additional pathway for harvesting hot electrons, which is enhanced through multiple reflections between the two barriers with different energy ranges. In addition, light absorption is improved by the band-to-band excitation of both semiconductors with different band gaps. Short-circuit current and energy conversion efficiency of the tandem-structured TiO2/Au/Si increased by 86% and 70%, respectively, compared with Au/Si metal/semiconductor nanodiodes, showing an overall solar energy conversion efficiency of 5.3%.

  7. Tandem-structured, hot electron based photovoltaic cell with double Schottky barriers

    PubMed Central

    Lee, Young Keun; Lee, Hyosun; Park, Jeong Young

    2014-01-01

    We demonstrate a tandem-structured, hot electron based photovoltaic cell with double Schottky barriers. The tandem-structured, hot electron based photovoltaic cell is composed of two metal/semiconductor interfaces. Two types of tandem cells were fabricated using TiO2/Au/Si and TiO2/Au/TiO2, and photocurrent enhancement was detected. The double Schottky barriers lead to an additional pathway for harvesting hot electrons, which is enhanced through multiple reflections between the two barriers with different energy ranges. In addition, light absorption is improved by the band-to-band excitation of both semiconductors with different band gaps. Short-circuit current and energy conversion efficiency of the tandem-structured TiO2/Au/Si increased by 86% and 70%, respectively, compared with Au/Si metal/semiconductor nanodiodes, showing an overall solar energy conversion efficiency of 5.3%. PMID:24694838

  8. Efficiently-designed hybrid tandem photovoltaic with organic and inorganic single cells

    NASA Astrophysics Data System (ADS)

    Vincent, Premkumar; Bae, Jin-Hyuk; Kim, Hyeok

    2016-05-01

    Conjugated polymers for solar-cell applications have been extensively studied and have proven highly beneficial in tandem solar-cell structures. This study focuses on achieving power conversion efficiencies of greater than 10% when in tandem with a highly efficient copper indium gallium diselenide (CIGS) solar cell. The optimal design is suggested based on the result of optical simulations on the organic-CIGS tandem structure. This is one of the first reports to show theoretically an organic-CIGS tandem solar cell to obtain an efficiency of greater than 10%. The best PCE was at a thickness of 200 nm for PTB7:PCBM, the active layer of the organic solar cell, and 400 nm for CIGS active layer. Our best datum showed an efficiency of 11.41% with a short-circuit current density of 11.56 mA/cm2 and a good spectral response at our optimized thicknesses.

  9. Versatile communication strategies among tandem WW domain repeats.

    PubMed

    Dodson, Emma Joy; Fishbain-Yoskovitz, Vered; Rotem-Bamberger, Shahar; Schueler-Furman, Ora

    2015-03-01

    Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands.

  10. MINIMARS: an attractive small tandem mirror fusion reactor

    SciTech Connect

    Perkins, L.J.; Logan, B.G.; Doggett, J.N.; Devoto, R.S.; Nelson, W.D.; Lousteau, D.C.; Kulcinski, G.L.; Santarius, J.F.; Gordon, J.D.; Campbell, R.B.

    1985-11-13

    Through the innovative design of a novel end plug scheme employing octopole MHD stabilization, we present the conceptual design of ''MIMIMARS'', a small commercial fusion reactor based on the tandem mirror principle. The current baseline for MINIMARS has a net electric output of 600 MWe and we have configured the design for short construction times, factory-built modules, inherently safe blanket systems, and multiplexing in station sizes of approx. 600 to 2400 MWe. We demonstrate that the compact octopole end cell provides a number of advantages over the more conventional quadrupole (yin-yang) end cell encountered in the MARS tandem mirror reactor study, and enables ignition to be achieved with much shorter central cell lengths. Accordingly, being economic in small sizes, MINIMARS provides an attractive alternative to the more conventional larger conceptual fusion reactors encountered to date, and would contribute significantly to the lowering of utility financial risk in a developing fusion economy.

  11. Versatile communication strategies among tandem WW domain repeats

    PubMed Central

    Dodson, Emma Joy; Fishbain-Yoskovitz, Vered; Rotem-Bamberger, Shahar

    2015-01-01

    Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands. PMID:25710931

  12. Tandem Repeats in Proteins: Prediction Algorithms and Biological Role

    PubMed Central

    Pellegrini, Marco

    2015-01-01

    Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR. PMID:26442257

  13. Nanocrystal assembly for tandem catalysis

    DOEpatents

    Yang, Peidong; Somorjai, Gabor; Yamada, Yusuke; Tsung, Chia-Kuang; Huang, Wenyu

    2014-10-14

    The present invention provides a nanocrystal tandem catalyst comprising at least two metal-metal oxide interfaces for the catalysis of sequential reactions. One embodiment utilizes a nanocrystal bilayer structure formed by assembling sub-10 nm platinum and cerium oxide nanocube monolayers on a silica substrate. The two distinct metal-metal oxide interfaces, CeO.sub.2--Pt and Pt--SiO.sub.2, can be used to catalyze two distinct sequential reactions. The CeO.sub.2--Pt interface catalyzed methanol decomposition to produce CO and H.sub.2, which were then subsequently used for ethylene hydroformylation catalyzed by the nearby Pt--SiO.sub.2 interface. Consequently, propanal was selectively produced on this nanocrystal bilayer tandem catalyst.

  14. Plasmonic polymer tandem solar cell.

    PubMed

    Yang, Jun; You, Jingbi; Chen, Chun-Chao; Hsu, Wan-Ching; Tan, Hai-ren; Zhang, Xing Wang; Hong, Ziruo; Yang, Yang

    2011-08-23

    We demonstrated plasmonic effects in an inverted tandem polymer solar cell configuration by blending Au nanoparticles (NPs) into the interconnecting layer (ICL) that connects two subcells. Experimental results showed this plasmonic enhanced ICL improves both the top and bottom subcells' efficiency simultaneously by enhancing optical absorption. The presence of Au NPs did not cause electrical characteristics to degrade within the tandem cell. As a result, a 20% improvement of power conversion efficiency has been attained by the light concentration of Au NPs via plasmonic near-field enhancement. The simulated near-field distribution and experimental Raman scattering investigation support our results of plasmonic induced enhancement in solar cell performance. Our finding shows a great potential of incorporating the plasmonic effect with conventional device structure in achieving highly efficient polymer solar cells. © 2011 American Chemical Society

  15. Tandem motors reduce well costs

    SciTech Connect

    Hooper, M.; Daigle, C.; Crowe, R.

    1995-10-01

    The new generation of tandem mud motors that recently appeared on the drilling scene is significantly affecting drilling efficiency worldwide. These motors provide drillers with increased horsepower at the bit, higher torque, and faster rates of penetration (ROP). With advanced engineering and more durable materials, motor life is being extended, thereby increasing the time between bit trips and reducing drilling costs. This article reviews the performance, design, and operation of these motors.

  16. Portable Tandem Mass Spectrometer Analyzer

    DTIC Science & Technology

    1991-07-01

    The planned instrument was to be small enough to be portable in small vehicles and was to be able to use either an atmospheric pressure ion source or a...conventional electron impact/chemical ionization ion source. In order to accomplish these developments an atmospheric pressure ionization source was...developed for a compact, commercially available tandem quadrupole mass spectrometer. This ion source could be readily exchanged with the conventional

  17. "Nanocrystal bilayer for tandem catalysis"

    SciTech Connect

    Yamada, Yusuke; Tsung, Chia Kuang; Huang, Wenyu; Huo, Ziyang; E.Habas, Susan E; Soejima, Tetsuro; Aliaga, Cesar E; Samorjai, Gabor A; Yang, Peidong

    2011-01-24

    Supported catalysts are widely used in industry and can be optimized by tuning the composition and interface of the metal nanoparticles and oxide supports. Rational design of metal-metal oxide interfaces in nanostructured catalysts is critical to achieve better reaction activities and selectivities. We introduce here a new class of nanocrystal tandem catalysts that have multiple metal-metal oxide interfaces for the catalysis of sequential reactions. We utilized a nanocrystal bilayer structure formed by assembling platinum and cerium oxide nanocube monolayers of less than 10 nm on a silica substrate. The two distinct metal-metal oxide interfaces, CeO2-Pt and Pt-SiO2, can be used to catalyse two distinct sequential reactions. The CeO2-Pt interface catalysed methanol decomposition to produce CO and H2, which were subsequently used for ethylene hydroformylation catalysed by the nearby Pt-SiO2 interface. Consequently, propanal was produced selectively from methanol and ethylene on the nanocrystal bilayer tandem catalyst. This new concept of nanocrystal tandem catalysis represents a powerful approach towards designing high-performance, multifunctional nanostructured catalysts

  18. Design optimization of thin-film/wafer-based tandem junction solar cells using analytical modeling

    NASA Astrophysics Data System (ADS)

    Davidson, Lauren; Toor, Fatima

    2016-03-01

    Several research groups are developing solar cells of varying designs and materials that are high efficiency as well as cost competitive with the single junction silicon (Si) solar cells commercially produced today. One of these solar cell designs is a tandem junction solar cell comprised of perovskite (CH3NH3PbI3) and silicon (Si). Loper et al.1 was able to create a 13.4% efficient tandem cell using a perovskite top cell and a Si bottom cell, and researchers are confident that the perovskite/Si tandem cell can be optimized in order to reach higher efficiencies without introducing expensive manufacturing processes. However, there are currently no commercially available software capable of modeling a tandem cell that is based on a thin-film based bottom cell and a wafer-based top cell. While PC1D2 and SCAPS3 are able to model tandem cells comprised solely of thin-film absorbers or solely of wafer-based absorbers, they result in convergence errors if a thin-film/wafer-based tandem cell, such as the perovskite/ Si cell, is modeled. The Matlab-based analytical model presented in this work is capable of modeling a thin-film/wafer-based tandem solar cell. The model allows a user to adjust the top and bottom cell parameters, such as reflectivity, material bandgaps, donor and acceptor densities, and material thicknesses, in order to optimize the short circuit current, open circuit voltage, and quantum efficiency of the tandem solar cell. Using the Matlab-based analytical model, we were able optimize a perovskite/Si tandem cell with an efficiency greater than 30%.

  19. Achieving 15% Tandem Polymer Solar Cells

    DTIC Science & Technology

    2015-06-23

    AFRL-OSR-VA-TR-2015-0145 Achieving 1% Tandem Polymer Solar Cells Yang Yang UNIVERSITY OF CALIFORNIA LOS ANGELES Final Report 06/23/2015 DISTRIBUTION...15% tandem polymer solar cells 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-12-1-0074 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER...1) develop novel low bandgap conjugated polymers for high efficiency tandem solar cell – single junction cell with 9% PCE achieved (2) develop

  20. Recent Activities at Tokai Tandem Accelerator

    SciTech Connect

    Ishii, Tetsuro

    2010-05-12

    Recent activities at the JAEA-Tokai tandem accelerator facility are presented. The terminal voltage of the tandem accelerator reached 19.1 MV by replacing acceleration tubes. The multi-charged positive-ion injector was installed in the terminal of the tandem accelerator, supplying high-current noble-gas ions. A superconducting cavity for low-velocity ions was developed. Radioactive nuclear beams of {sup 8,9}Li and fission products, produced by the tandem accelerator and separated by the ISOL, were supplied with experiment. Recent results of nuclear physics experiments are reported.

  1. Detecting long tandem duplications in genomic sequences

    PubMed Central

    2012-01-01

    Background Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. Results In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,a we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS < 1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. Conclusions ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations. PMID:22568762

  2. The characterization of tandem and corrugated wings

    NASA Astrophysics Data System (ADS)

    Lian, Yongsheng; Broering, Timothy; Hord, Kyle; Prater, Russell

    2014-02-01

    Dragonfly wings have two distinct features: a tandem configuration and wing corrugation. Both features have been extensively studied with the aim to understand the superior flight performance of dragonflies. In this paper we review recent development of tandem and corrugated wing aerodynamics. With regards to the tandem configuration, this review will focus on wing/wing and wing/vortex interactions at different flapping modes and wing spacing. In addition, the aerodynamics of tandem wings under gusty conditions will be reviewed and compared with isolated wings to demonstrate the gust resistance characteristics of flapping wings. Regarding corrugated wings, we review their structural and aerodynamic characteristics.

  3. 47 CFR 69.111 - Tandem-switched transport and tandem charge.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... circuits used in the tandem to end office links (or a surrogate based on the proportion of copper and fiber... the relative number of DS1 and DS3 circuits used in the tandem to end office links (or a surrogate... circuits used in the tandem to end office links (or a surrogate based on the proportion of copper and...

  4. 47 CFR 69.111 - Tandem-switched transport and tandem charge.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... circuits used in the tandem to end office links (or a surrogate based on the proportion of copper and fiber... the relative number of DS1 and DS3 circuits used in the tandem to end office links (or a surrogate... circuits used in the tandem to end office links (or a surrogate based on the proportion of copper and...

  5. Electrolytes based on TEMPO-Co tandem redox systems outperform single redox systems in dye-sensitized solar cells.

    PubMed

    Cong, Jiayan; Hao, Yan; Boschloo, Gerrit; Kloo, Lars

    2015-01-01

    A new TEMPO-Co tandem redox system with TEMPO and Co(bpy)3 (2+/3+) has been investigated for the use in dye-sensitized solar cells (DSSCs). A large open-circuit voltage (VOC ) increase, from 862 mV to 965 mV, was observed in the tandem redox system, while the short-circuit current density (JSC ) was maintained. The conversion efficiency was observed to increase from 7.1 % for cells containing the single Co(bpy)3 (2+/3+) redox couple, to 8.4 % for cells containing the TEMPO-Co tandem redox system. The reason for the increase in VOC and overall efficiency is ascribed to the involvement of partial regeneration of the sensitizing dye molecules by TEMPO. This assumption can be verified through the observed much faster regeneration dynamics exhibited in the presence of the tandem system. Using the tandem redox system, the faster recombination problem of the single TEMPO redox couple is resolved and the mass-transport of the metal-complex-based electrolyte is also improved. This TEMPO-Co tandem system is so far the most efficient tandem redox electrolyte reported not involving iodine. The current results show a promising future for tandem system as replacements for single redox systems in electrolytes for DSSCs.

  6. Tandem mirror technology demonstration facility

    SciTech Connect

    Not Available

    1983-10-01

    This report describes a facility for generating engineering data on the nuclear technologies needed to build an engineering test reactor (ETR). The facility, based on a tandem mirror operating in the Kelley mode, could be used to produce a high neutron flux (1.4 MW/M/sup 2/) on an 8-m/sup 2/ test area for testing fusion blankets. Runs of more than 100 h, with an average availability of 30%, would produce a fluence of 5 mW/yr/m/sup 2/ and give the necessary experience for successful operation of an ETR.

  7. Facile Synthesis of Carbazoles via a Tandem Iodocyclization with 1,2-Alkyl Migration and Aromatization.

    PubMed

    Wang, Jia; Zhu, Hai-Tao; Qiu, Yi-Feng; Niu, Yuan; Chen, Si; Li, Ying-Xiu; Liu, Xue-Yuan; Liang, Yong-Min

    2015-06-19

    A strategy for the synthesis of iodocarbazoles through a tandem iodocyclization with migration and aromatization is presented. This sequential cascade process is concisely conducted at room temperature and in a short time. Moreover, the obtained halides can be further applied to palladium-catalyzed coupling reactions, which act as the important intermediates for building other valuable compounds.

  8. On the trajectory scaling of tandem twin jets in cross-flow in close proximity

    NASA Astrophysics Data System (ADS)

    New, T. H.; Zang, B.

    2015-11-01

    An experimental study has been conducted on tandem twin jets in cross-flow (JICF) in close proximity to investigate the relationships between their trajectories, separation distances and velocity ratios. Results show that the front and rear jets, each with initially distinct jet trajectory, merge into a single trajectory shortly after they exhaust into the cross-flow. Furthermore, the merged tandem JICF attains deeper cross-flow penetration than that of a single JICF at the same velocity ratio. The front jet is also observed to provide `shielding' for the rear jet such that the latter penetrates relatively deeper into the cross-flow, which corroborates observations made by earlier studies. In particular, the present study demonstrates that it is possible to collapse the tandem JICF merged trajectories by ` rD'-scaling, where A and B coefficients show slight reductions and increments, respectively, with increasing separation distance. Collapsing the merged trajectories by using single JICF A and B coefficients leads to the notion of effective velocity ratio for tandem JICF, which enable the authors to propose a modification in the ` rD'-scaling law for tandem JICF. Lastly, the modified ` rD'-scaling law is applied to trajectory data from an earlier tandem JICF study, and its validity is demonstrated by the resulting good collapse.

  9. Multistage regulator based on tandem promoters and CRISPR/Cas.

    PubMed

    Jia, Hangxing; Liang, Tong; Wang, Zhaoning; He, Zhaoren; Liu, Yang; Yang, Lei; Zeng, Yan; Liu, Shaopeng; Tang, Linyi; Wang, Jianbo; Chen, Yu; Xie, Zhixiong

    2014-12-19

    Accurately controlling expression of target genes between several designed levels is essential for low-noise gene network and dynamic range of gene expression. However, such manipulations have been hard to achieve due to technical limitations. Based on tandem promoters and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) system, we constructed a multistage regulator that could stably regulate the expression of the reporter gene on three levels, with more than 2-fold difference between each of them. Our findings provide novel insights into constructing a more powerful gene regulation system.

  10. Argonne Tandem-Linac Accelerator System

    SciTech Connect

    Bollinger, L.M.

    1983-01-01

    Design considerations and operational experience for the existing heavy-ion accelerator consisting of a tandem injecting into a superconducting linac are summarized, with emphasis on the general features of the system. This introduction provides the basis for a discussion of the objectives and design of ATLAS, a larger tandem-linac system being formed by expanding the existing superconducting linac.

  11. 33 CFR 401.41 - Tandem lockage.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Tandem lockage. 401.41 Section 401.41 Navigation and Navigable Waters SAINT LAWRENCE SEAWAY DEVELOPMENT CORPORATION, DEPARTMENT OF TRANSPORTATION SEAWAY REGULATIONS AND RULES Regulations Seaway Navigation § 401.41 Tandem lockage. Where two or...

  12. Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases

    PubMed Central

    2012-01-01

    Background Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters. Results In this paper we present TReaDS - Tandem Repeats Discovery Service, a tandem repeat meta search engine. TReaDS forwards user requests to several state of the art tools for finding tandem repeats and merges their outcome into a single report, providing a global, synthetic, and comparative view of the results. In particular, TReaDS allows the user to (i) simultaneously run different algorithms on the same data set, (ii) choose for each algorithm a different setting of parameters, and (iii) obtain a report that can be downloaded for further, off-line, investigations. We used TReaDS to investigate sequences associated with repeat expansion diseases. Conclusions By using the tool TReaDS we discover that, for 27 repeat expansion diseases out of a currently known set of 29, long fuzzy tandem repeats are covering the expansion loci. Tests with control sets confirm the specificity of this association. This finding suggests that long fuzzy tandem repeats can be a new class of cis-acting elements involved in the mechanisms leading to the expansion instability. We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simplifies the burden of comparing and merging the results, thus expanding our

  13. Photoelectrochemical and photovoltaic characteristics of amorphous-silicon-based tandem cells as photocathodes for water splitting.

    PubMed

    Ziegler, Jürgen; Kaiser, Bernhard; Jaegermann, Wolfram; Urbain, Félix; Becker, Jan-Philipp; Smirnov, Vladimir; Finger, Friedhelm

    2014-12-15

    In this study amorphous silicon tandem solar cells are successfully utilized as photoelectrodes in a photoelectrochemical cell for water electrolysis. The tandem cells are modified with various amounts of platinum and are combined with a ruthenium oxide counter electrode. In a two-electrode arrangement this system is capable of splitting water without external bias with a short-circuit current of 4.50 mA cm(-2). On the assumption that no faradaic losses occur, a solar-to-hydrogen efficiency of 5.54% is achieved. In order to identify the relevant loss processes, additional three-electrode measurements were performed for each involved half-cell.

  14. Label-free electrochemical nucleic acid biosensing by tandem polymerization and cleavage-mediated cascade target recycling and DNAzyme amplification.

    PubMed

    Liu, Shufeng; Gong, Hongwei; Wang, Yanqun; Wang, Li

    2016-03-15

    Owing to the intrinsic importance of nucleic acid as bio-targets, the achievement of its simple and sensitive detection with high confidence is very essential for biological studies and diagnostic purposes. Herein, a label-free, isothermal, and ultrasensitive electrochemical detection of target DNA was developed by using a tandem polymerization and cleavage-mediated cascade target recycling and DNAzyme releasing amplification strategy. Upon sensing of the nucleic acid analyte for the assembled hairpin-like probe DNA on the electrode, the DNA polymerase guided the target recycling and simultaneously triggered the lambda exonuclease cleavage, accompanied by the cascade recycling of the released new complementary strand and the amplified liberation of the G-rich sequence of the HRP-mimicking DNAzyme. The electrocatalytic reduction of H2O2 by the generated hemin/G-quadruplex DNAzyme was used for the signal readout and further amplification toward target response. Such tandem functional operation by DNA polymerase, lambda exonuclease and DNAzyme endows the developed biosensor with a high sensitivity and also a high confidence. A low detection limit of 5 fM with an excellent selectivity toward target DNA could be achieved. It also exhibits the distinct advantages of simplicity in probe design and biosensor fabrication, and label-free electrochemical detection, thus may offer a promising avenue for the applications in disease diagnosis and clinical biomedicine. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Tandem Mirror Reactor Systems Code (Version I)

    SciTech Connect

    Reid, R.L.; Finn, P.A.; Gohar, M.Y.; Barrett, R.J.; Gorker, G.E.; Spampinaton, P.T.; Bulmer, R.H.; Dorn, D.W.; Perkins, L.J.; Ghose, S.

    1985-09-01

    A computer code was developed to model a Tandem Mirror Reactor. Ths is the first Tandem Mirror Reactor model to couple, in detail, the highly linked physics, magnetics, and neutronic analysis into a single code. This report describes the code architecture, provides a summary description of the modules comprising the code, and includes an example execution of the Tandem Mirror Reactor Systems Code. Results from this code for two sensitivity studies are also included. These studies are: (1) to determine the impact of center cell plasma radius, length, and ion temperature on reactor cost and performance at constant fusion power; and (2) to determine the impact of reactor power level on cost.

  16. Characterization of the DNA-binding properties of the myeloid zinc finger protein MZF1: two independent DNA-binding domains recognize two DNA consensus sequences with a common G-rich core.

    PubMed Central

    Morris, J F; Hromas, R; Rauscher, F J

    1994-01-01

    The myeloid zinc finger gene 1, MZF1, encodes a transcription factor which is expressed in hematopoietic progenitor cells that are committed to myeloid lineage differentiation. MZF1 contains 13 C2H2 zinc fingers arranged in two domains which are separated by a short glycine- and proline-rich sequence. The first domain consists of zinc fingers 1 to 4, and the second domain is formed by zinc fingers 5 to 13. We have determined that both sets of zinc finger domains bind DNA. Purified, recombinant MZF1 proteins containing either the first set of zinc fingers or the second set were prepared and used to affinity select DNA sequences from a library of degenerate oligonucleotides by using successive rounds of gel shift followed by PCR amplification. Surprisingly, both DNA-binding domains of MZF1 selected similar DNA-binding consensus sequences containing a core of four or five guanine residues, reminiscent of an NF-kappa B half-site: 1-4, 5'-AGTGGGGA-3'; 5-13, 5'-CGGGnGAGGGGGAA-3'. The full-length MZF1 protein containing both sets of zinc finger DNA-binding domains recognizes synthetic oligonucleotides containing either the 1-4 or 5-13 consensus binding sites in gel shift assays. Thus, we have identified the core DNA consensus binding sites for each of the two DNA-binding domains of a myeloid-specific zinc finger transcription factor. Identification of these DNA-binding sites will allow us to identify target genes regulated by MZF1 and to assess the role of MZF1 as a transcriptional regulator of hematopoiesis. Images PMID:8114711

  17. Tandem mirror reactors with thermal barriers

    SciTech Connect

    Logan, B.G.; Arfin, B.; Barr, W.L.

    1980-05-23

    Preliminary calculations of Q and magnet designs are presented for three different versions of tandem mirror reactors (TMR) using thermal barriers to enhance plug potentials by auxiliary electron heating. These three versions, called A-cell-barrier TMR, axisymmetric-barrier TMR, and inside-barrier TMR, exhibit reduced plug density (n/sub p/ << 10/sup 19/ m/sup -3/) and less required magnetic mirror field (B/sub mirror approx. = 9 T) compared to TMR designs without thermal barriers. A-cell barrier TMR Q's range from 5 to 25 depending on the central-cell length (L/sub c/ = 100 to 200 m) and peak center-cell beta ..beta../sub c/ (0.3 to 0.7) allowed by MHD stability. Axisymmetric-barrier TMR Q's range from 14 at L/sub c/ = 100 m to 30 at L/sub c/ = 200 m, if peak ..beta../sub c/ = 1. From a global equilibrium model for the inside-barrier TMR, Q values greater than 15 are achieved for ..nu.. = 0.5 in the modified Boltzmann relation for the plug potential. Even higher Q's are obtained using ECRF heating in the barrier to create a hot, mirror-trapped electron population. TMR's burning D-D as a fuel have been analyzed with a modified version of the global equilibrium model and under the assumption of an axisymmetric plug and barrier stabilized by surface magnetic fields. High-barrier mirror ratio is now feasible (R/sub b/ = 30-50), and short barrier length permits Q/sub DD/ values greater than 5.

  18. TRDB—The Tandem Repeats Database

    PubMed Central

    Gelfand, Yevgeniy; Rodriguez, Alfredo; Benson, Gary

    2007-01-01

    Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA. It contains a variety of tools for repeat analysis, including the Tandem Repeats Finder program, query and filtering capabilities, repeat clustering, polymorphism prediction, PCR primer selection, data visualization and data download in a variety of formats. In addition, TRDB serves as a centralized research workbench. It provides user storage space and permits collaborators to privately share their data and analysis. TRDB is available at . PMID:17175540

  19. 33 CFR 401.41 - Tandem lockage.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... TRANSPORTATION SEAWAY REGULATIONS AND RULES Regulations Seaway Navigation § 401.41 Tandem lockage. Where two or... stop a sufficient distance from the preceding vessel to avoid a collision; and (b) Be moved...

  20. Oak Ridge 25-MV tandem accelerator

    SciTech Connect

    Jones, C.M.

    1981-01-01

    A brief description is presented of the scope and status of the heavy ion accelerator facility, and status of the project is discussed. Initial operation of the 25 MV tandem accelerator from National Electrostatics Corporation is covered. (GHT)

  1. Ligand Binding to WW Tandem Domains of YAP2 Transcriptional Regulator Is Under Negative Cooperativity

    PubMed Central

    Schuchardt, Brett J.; Mikles, David C.; Hoang, Lawrence M.; Bhat, Vikas; McDonald, Caleb B.; Sudol, Marius; Farooq, Amjad

    2014-01-01

    YAP2 transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well-documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules. PMID:25283809

  2. Organic-inorganic halide perovskite/crystalline silicon four-terminal tandem solar cells.

    PubMed

    Löper, Philipp; Moon, Soo-Jin; de Nicolas, Sílvia Martín; Niesen, Bjoern; Ledinsky, Martin; Nicolay, Sylvain; Bailat, Julien; Yum, Jun-Ho; De Wolf, Stefaan; Ballif, Christophe

    2015-01-21

    Tandem solar cells constructed from a crystalline silicon (c-Si) bottom cell and a low-cost top cell offer a promising way to ensure long-term price reductions of photovoltaic modules. We present a four-terminal tandem solar cell consisting of a methyl ammonium lead triiodide (CH3NH3PbI3) top cell and a c-Si heterojunction bottom cell. The CH3NH3PbI3 top cell exhibits broad-band transparency owing to its design free of metallic components and yields a transmittance of >55% in the near-infrared spectral region. This allows the generation of a short-circuit current density of 13.7 mA cm(-2) in the bottom cell. The four-terminal tandem solar cell yields an efficiency of 13.4% (top cell: 6.2%, bottom cell: 7.2%), which is a gain of 1.8%abs with respect to the reference single-junction CH3NH3PbI3 solar cell with metal back contact. We employ the four-terminal tandem solar cell for a detailed investigation of the optical losses and to derive guidelines for further efficiency improvements. Based on a power loss analysis, we estimate that tandem efficiencies of ∼28% are attainable using an optically optimized system based on current technology, whereas a fully optimized, ultimate device with matched current could yield up to 31.6%.

  3. Ligand binding to WW tandem domains of YAP2 transcriptional regulator is under negative cooperativity.

    PubMed

    Schuchardt, Brett J; Mikles, David C; Hoang, Lawrence M; Bhat, Vikas; McDonald, Caleb B; Sudol, Marius; Farooq, Amjad

    2014-12-01

    YES-associated protein 2 (YAP2) transcriptional regulator drives a multitude of cellular processes, including the newly discovered Hippo tumor suppressor pathway, by virtue of the ability of its WW domains to bind and recruit PPXY-containing ligands to specific subcellular compartments. Herein, we employ an array of biophysical tools to investigate allosteric communication between the WW tandem domains of YAP2. Our data show that the WW tandem domains of YAP2 negatively cooperate when binding to their cognate ligands. Moreover, the molecular origin of such negative cooperativity lies in an unfavorable entropic contribution to the overall free energy relative to ligand binding to isolated WW domains. Consistent with this notion, the WW tandem domains adopt a fixed spatial orientation such that the WW1 domain curves outwards and stacks onto the binding groove of the WW2 domain, thereby sterically hindering ligand binding to both itself and its tandem partner. Although ligand binding to both WW domains disrupts such interdomain stacking interaction, they reorient themselves and adopt an alternative fixed spatial orientation in the liganded state by virtue of their ability to engage laterally so as to allow their binding grooves to point outwards and away from each other. In short, while the ability of WW tandem domains to aid ligand binding is well documented, our demonstration that they may also be subject to negative binding cooperativity represents a paradigm shift in our understanding of the molecular action of this ubiquitous family of protein modules.

  4. High-Efficiency Nonfullerene Organic Solar Cells with a Parallel Tandem Configuration.

    PubMed

    Zuo, Lijian; Yu, Jiangsheng; Shi, Xueliang; Lin, Francis; Tang, Weihua; Jen, Alex K-Y

    2017-09-01

    In this work, a highly efficient parallel connected tandem solar cell utilizing a nonfullerene acceptor is demonstrated. Guided by optical simulation, each of the active layer thicknesses of subcells are tuned to maximize its light trapping without spending intense effort to match photocurrent. Interestingly, a strong optical microcavity with dual oscillation centers is formed in a back subcell, which further enhances light absorption. The parallel tandem device shows an improved photon-to-electron response over the range between 450 and 800 nm, and a high short-circuit current density (J SC ) of 17.92 mA cm(-2) . In addition, the subcells show high fill factors due to reduced recombination loss under diluted light intensity. These merits enable an overall power conversion efficiency (PCE) of >10% for this tandem cell, which represents a ≈15% enhancement compared to the optimal single-junction device. Further application of the designed parallel tandem configuration to more efficient single-junction cells enable a PCE of >11%, which is the highest efficiency among all parallel connected organic solar cells (OSCs). This work stresses the importance of employing a parallel tandem configuration for achieving efficient light harvesting in nonfullerene-based OSCs. It provides a useful strategy for exploring the ultimate performance of organic solar cells. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Tandem Spinal Stenosis: A Systematic Review.

    PubMed

    Overley, Samuel C; Kim, Jun S; Gogel, Brooke A; Merrill, Robert K; Hecht, Andrew C

    2017-09-05

    Tandem spinal stenosis refers to spinal canal diameter narrowing in at least 2 distinct regions of the spine, most commonly the lumbar and cervical regions. This entity can be an asymptomatic radiographic finding, or it can present with severe myelopathy and lower-extremity symptoms. Tandem spinal stenosis may impact surgeon decision-making when planning either cervical or lumbar spine surgery, and there is currently no consensus in the literature regarding the treatment algorithm for operative intervention. A MEDLINE literature search was performed using PubMed, the Cochrane Database of Systematic Reviews, and Embase from January 1980 to February 2015 using Medical Subject Heading queries for the terms "tandem spinal stenosis," "cervical stenosis AND lumbar stenosis," and "concomitant spinal stenosis." We included studies involving adult patients, tandem spinal stenosis of the cervical and lumbar regions, and a minimum of 5 patients. Articles that did not discuss spinal disorders or only explored disorders at a single spinal region were excluded. The initial database review resulted in 234 articles. After abstracts were reviewed, only 17 articles that met inclusion criteria were identified: 2 cadaveric studies, 5 clinical studies of patients with radiographic tandem spinal stenosis, and 10 clinical studies of patients with symptomatic tandem spinal stenosis. Tandem spinal stenosis is a common condition present in up to 60% of patients with spinal stenosis. This disorder, however, is often overlooked, which can lead to serious complications. Identification of tandem spinal stenosis is paramount as a first step in management and, although there is still no preferred intervention, both staged and simultaneous procedures have been shown to be effective. Surgeons may utilize a single, staged, or combined approach to decompression, always addressing cervical myelopathy as a priority.

  6. A Comparison of Tandem Walk Performance Between Bed Rest Subjects and Astronauts

    NASA Technical Reports Server (NTRS)

    Miller, Chris; Peters, Brian; Kofman, Igor; Philips, Tiffany; Batson, Crystal; Cerisano, Jody; Fisher, Elizabeth; Mulavara, Ajitkumar; Feiveson, Alan; Reschke, Millard; Bloomberg, Jacob

    2015-01-01

    Astronauts experience a microgravity environment during spaceflight, which results in a central reinterpretation of both vestibular and body axial-loading information by the sensorimotor system. Subjects in bed rest studies lie at 6deg head-down in strict bed rest to simulate the fluid shift and gravity-unloading of the microgravity environment. However, bed rest subjects still sense gravity in the vestibular organs. Therefore, bed rest isolates the axial-unloading component, thus allowing for the direct study of its effects. The Tandem Walk is a standard sensorimotor test of dynamic postural stability. In a previous abstract, we compared performance on a Tandem Walk test between bed rest control subjects, and short- and long-duration astronauts both before and after flight/bed rest using a composite index of performance, called the Tandem Walk Parameter (TWP), that takes into account speed, accuracy, and balance control. This new study extends the previous data set to include bed rest subjects who performed exercise countermeasures. The purpose of this study was to compare performance during the Tandem Walk test between bed rest subjects (with and without exercise), short-duration (Space Shuttle) crewmembers, and long-duration International Space Station (ISS) crewmembers at various time points during their recovery from bed rest or spaceflight.

  7. Short stature

    MedlinePlus

    ... medical condition. Bone or skeletal disorders, such as: Rickets Achondroplasia Chronic diseases, such as: Asthma Celiac disease ... the evaluation of symptomatic short children. J Pediatr . 2013;163:1045. PMID: 23706358 www.ncbi.nlm.nih. ...

  8. Gyrokinetic equilibrium and stability in quadrupole tandem mirrors

    SciTech Connect

    Bulmer, R.H.; Kaiser, T.B.; Nevins, W.M.; Newcomb, W.A.; Pearlstein, L.D.; Strauss, H.R.; Wollman, S.; Wakatani, M.

    1982-08-02

    This paper discusses recent theoretical work on the equilibrium and stability of quadrupole tandem mirrors in the paraxial limit. It reviews calculations of three-dimensional equilibria by means of a ..beta..-expansion technique which lead to an understanding of the important role played by parallel currents and the corollary importance of careful design of the structure of the vacuum geodesic curvature. The previously predicted scaling with central-cell length of the finite-..beta.. distortion of vacuum flux surfaces is shown to saturate because of finite orbit effects. An adaptation to tandem geometries of the reduced MHD technique for calculating high-..beta.. three-dimensional equilibria is described. This approach uses the paraxial expansion to resolve the time-dependent relaxation to equilibrium into three distinct timescales on which the motion can be followed independently. Regarding stability, it is shown that kinetic effects suppress ballooning modes of short-to-moderate perpendicular wavelength; in the limit that such effects are dominant only rigid modes are possible. The stability of the latter modes is investigated within the context of the energy principle. Results of equilibrium and stability calculations for the TMX-U and MFTF-B experiments at Livermore are presented.

  9. Tandem Organic Light-Emitting Diodes.

    PubMed

    Fung, Man-Keung; Li, Yan-Qing; Liao, Liang-Sheng

    2016-12-01

    A tandem organic light-emitting diode (OLED) is an organic optoelectronic device that has two or more electroluminescence (EL) units connected electrically in series with unique intermediate connectors within the device. Researchers have studied this new OLED architecture with growing interest and have found that the current efficiency of a tandem OLED containing N EL units (N > 1) should be N times that of a conventional OLED containing only a single EL unit. Therefore, this new architecture is potentially useful for constructing high-efficiency, high-luminance, and long-lifetime OLED displays and organic solid-state lighting sources. In a tandem OLED, the intermediate connector plays a crucial role in determining the effectiveness of the stacked EL units. The interfaces in the connector control the inner charge generation and charge injection into the adjacent EL units. Meanwhile, the transparency and the thickness of the connector affect the light output of the device. Therefore, the intermediate connector should be made to meet both the electrical and optical requirements for achieving optimal performance. Here, recent advances in the research of the tandem OLEDs is discussed, with the main focus on material selection and interface studies in the intermediate connectors, as well as the optical design of the tandem OLEDs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. A region of euchromatin coincides with an extensive tandem repeat on the mouse (Mus musculus) inactive X chromosome.

    PubMed

    Darrow, Emily M; Seberg, Andrew P; Das, Sunny; Figueroa, Debbie M; Sun, Zhuo; Moseley, Shawn C; Chadwick, Brian P

    2014-09-01

    Euchromatic features are largely absent from the human inactive X chromosome (Xi), with the exception of several large tandem repeats that can be detected as euchromatin bands at metaphase. Despite residing megabases apart, these tandem repeats make frequent inactive X-specific interactions. The mouse homologue has been reported for at least one of the tandem repeats, but whether the mouse Xi is also characterized by distinct bands of euchromatin remains unknown. We examined the mouse Xi for the presence of euchromatin bands by examining the pattern of histone H3 dimethylated at lysine 4 and detected two major signals. The first band resides in the subtelomeric region of band XF5 and may correspond to the pseudoautosomal region. The second band localizes to XE3 and coincides with an extensive complex repeat composed of a large tandem and inverted repeat segment as well as several large short interspersed nuclear element (SINE)-rich tandem repeats. Fluorescence in situ hybridization reveals that sequences with homology to the repeat region are scattered along the length of the Y chromosome. Immunofluorescence analysis of histone H3 trimethylated at lysine 9 on metaphase chromosomes indicates that the repeat region corresponds to a band of constitutive heterochromatin on the male X and female active X chromosomes, whereas the euchromatin signal appears to be female specific. These data suggest that the band of euchromatin observed at XE3 is unique to the mouse Xi, comparable to the chromatin arrangement of several large tandem repeats located on the human X chromosome.

  11. Detection of protein-protein interactions using tandem affinity purification.

    PubMed

    Goodfellow, Ian; Bailey, Dalan

    2014-01-01

    Tandem affinity purification (TAP) is an invaluable technique for identifying interaction partners for an affinity tagged bait protein. The approach relies on the fusion of dual tags to the bait before separate rounds of affinity purification and precipitation. Frequently two specific elution steps are also performed to increase the specificity of the overall technique. In the method detailed here, the two tags used are protein G and a short streptavidin binding peptide; however, many variations can be employed. In our example the tags are separated by a cleavable tobacco etch virus protease target sequence, allowing for specific elution after the first round of affinity purification. Proteins isolated after the final elution step in this process are concentrated before being identified by mass spectrometry. The use of dual affinity tags and specific elution in this technique dramatically increases both the specificity and stringency of the pull-downs, ensuring a low level of background nonspecific interactions.

  12. Halide Perovskites for Tandem Solar Cells.

    PubMed

    Lee, Jin-Wook; Hsieh, Yao-Tsung; De Marco, Nicholas; Bae, Sang-Hoon; Han, Qifeng; Yang, Yang

    2017-05-04

    Perovskite solar cells have become one of the strongest candidates for next-generation solar energy technologies. A myriad of beneficial optoelectronic properties of the perovskite materials have enabled superb power conversion efficiencies (PCE) exceeding 22% for a single-junction device. The high PCE achievable via low processing costs and relatively high variability in optical properties have opened new possibilities for perovskites in tandem solar cells. In this Perspective, we will discuss current research trends in fabricating tandem perovskite-based solar cells in combination with a variety of mature photovoltaic devices such as organic, silicon, and Cu(In,Ga)(S,Se)2 (CIGS) solar cells. Characteristic features and present limitations of each tandem cell will be discussed and elaborated upon. Finally, key issues for further improvement and the future outlook will be discussed.

  13. [Enrichment of extracellular DNA from the cultivation medium of human peripheral blood mononuclears with genomic CpG rich fragments results in increased cell production of IL-6 and TNF-a via activation of the NF-kB signaling pathway].

    PubMed

    Speranskii, A I; Kostyuk, S V; Kalashnikova, E A; Veiko, N N

    2016-03-01

    Previously, it was found that blood plasma extracellular DNA (ecDNA) of patients with rheumatoid arthritis (RA) is enriched with CpG-rich genomic DNA fragments, which contain TLR9 ligands (Veiko et al., 2006). In this study we have demonstrated that ecDNA of a RA patient and model fragments added to a cultivation medium of peripheral blood mononuclear cells (PBMC) of healthy donors stimulate expression of genes for the TLR9-MyD88-NF-kB signaling pathway; this leads to a significant increase in concentrations of the proinflammatory cytokines IL-6 and TNF-a in the cultivation medium. Human genomic DNA non-enriched with the CpG sequences did not stimulate IL-6 and TNF-a synthesis in PBMC. A scheme explaining the potential role ecDNA in the induction and maintenance of increased levels of the proinflammatory cytokines under conditions damaging the human cells has been proposed.

  14. High performance polymer tandem solar cell

    PubMed Central

    da Silva, Wilson Jose; Schneider, Fabio Kurt; Mohd Yusoff, Abd. Rashid bin; Jang, Jin

    2015-01-01

    A power conversion efficiency of 9.02% is obtained for a fully solution-processed polymer tandem solar cell, based on the diketopyrrolopyrrole unit polymer as a low bandgap photoactive material in the rear subcell, in conjunction with a new robust interconnecting layer. This interconnecting layer is optically transparent, electrically conductive, and physically strong, thus, the charges can be collected and recombined in the interconnecting layer under illumination, while the charge is generated and extracted under dark conditions. This indicates that careful interface engineering of the charge-carrier transport layer is a useful approach to further improve the performance of polymer tandem solar cells. PMID:26669577

  15. Tandem mirror thermal barrier experimental program plan

    SciTech Connect

    Coensgen, F.H.; Drake, R.P.; Simonen, T.C.

    1980-01-02

    This report describes an experimental plan for the development of the Tandem Mirror Thermal Barrier. Included is: (1) a description of thermal barrier related physics experiments; (2) thermal barrier related experiments in the existing TMX and Phaedrus experiments; (3) a thermal barrier TMX upgrade; and (4) initiation of investigations of axisymmetric magnetic geometry. Experimental studies of the first two items are presently underway. Results are expected from the TMX upgrade by the close of 1981 and from axisymmetric tandem mirror experiments at the end of 1983. Plans for Phaedrus upgrades are developing for the same period.

  16. Tandem-mirror program: status and projection

    SciTech Connect

    Van Atta, C.M.

    1981-03-12

    Construction of MFTF-B is scheduled for completion in 1985. Results of experiments in TMX-U and MFTF-B will permit the design of the D-T burning tandem-mirror next-step facility (TMNS) in which physics issues will not be at issue. TMNS will be a facility for engineering research and development. The end cells of TMNS are expected to be appropriate for a tandem-mirror demonstration fusion reactor (TMR), construction of which should begin about 1986 for operation in the 1990's.

  17. High voltage series connected tandem junction solar battery

    DOEpatents

    Hanak, Joseph J.

    1982-01-01

    A high voltage series connected tandem junction solar battery which comprises a plurality of strips of tandem junction solar cells of hydrogenated amorphous silicon having one optical path and electrically interconnected by a tunnel junction. The layers of hydrogenated amorphous silicon, arranged in a tandem configuration, can have the same bandgap or differing bandgaps. The tandem junction strip solar cells are series connected to produce a solar battery of any desired voltage.

  18. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Canard or tandem wing configurations. 23... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem wing configuration must: (a) Meet all requirements of subpart C and subpart D of this part applicable to a wing;...

  19. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 1 2012-01-01 2012-01-01 false Canard or tandem wing configurations. 23... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem wing configuration must: (a) Meet all requirements of subpart C and subpart D of this part applicable to a wing;...

  20. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Canard or tandem wing configurations. 23... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem wing configuration must: (a) Meet all requirements of subpart C and subpart D of this part applicable to a wing;...

  1. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 1 2014-01-01 2014-01-01 false Canard or tandem wing configurations. 23... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem wing configuration must: (a) Meet all requirements of subpart C and subpart D of this part applicable to a wing;...

  2. 14 CFR 23.302 - Canard or tandem wing configurations.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 1 2013-01-01 2013-01-01 false Canard or tandem wing configurations. 23... General § 23.302 Canard or tandem wing configurations. The forward structure of a canard or tandem wing configuration must: (a) Meet all requirements of subpart C and subpart D of this part applicable to a wing;...

  3. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 2 2012-01-01 2012-01-01 false Use of tandem parachute systems. 105.45... (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES PARACHUTE OPERATIONS Parachute Equipment and Packing § 105.45 Use of tandem parachute systems. (a) No person may conduct a parachute operation using a tandem...

  4. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 2 2011-01-01 2011-01-01 false Use of tandem parachute systems. 105.45... (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES PARACHUTE OPERATIONS Parachute Equipment and Packing § 105.45 Use of tandem parachute systems. (a) No person may conduct a parachute operation using a tandem...

  5. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 2 2013-01-01 2013-01-01 false Use of tandem parachute systems. 105.45... (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES PARACHUTE OPERATIONS Parachute Equipment and Packing § 105.45 Use of tandem parachute systems. (a) No person may conduct a parachute operation using a tandem...

  6. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 2 2014-01-01 2014-01-01 false Use of tandem parachute systems. 105.45... (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES PARACHUTE OPERATIONS Parachute Equipment and Packing § 105.45 Use of tandem parachute systems. (a) No person may conduct a parachute operation using a tandem...

  7. 47 CFR 69.129 - Signalling for tandem switching.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 3 2013-10-01 2013-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. ...

  8. 47 CFR 69.129 - Signalling for tandem switching.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 3 2010-10-01 2010-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. ...

  9. 47 CFR 69.129 - Signalling for tandem switching.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 3 2012-10-01 2012-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. ...

  10. 47 CFR 69.129 - Signalling for tandem switching.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 3 2011-10-01 2011-10-01 false Signalling for tandem switching. 69.129 Section... (CONTINUED) ACCESS CHARGES Computation of Charges § 69.129 Signalling for tandem switching. A charge that is... provision of signalling for tandem switching. ...

  11. Model development of monolithic tandem silicon-perovskite solar cell by SCAPS simulation

    NASA Astrophysics Data System (ADS)

    Ramli, Noor Fadhilah; Sepeai, Suhaila; Rostan, Nur Fairuz Mohd; Ludin, Norasikin Ahmad; Ibrahim, Mohd. Adib; Teridi, Mohd Asri Mat; Zaidi, Salem H.

    2017-05-01

    Organic-inorganic lead halide perovskites have significant role in the photovoltaic (PV) technology due to its high efficiency, lightweight and cost effectiveness especially methyl ammonium lead (II) iodide (MALI). The MALI can act as absorber layer which has a band gap of 1.5 eV which is compatible to be paired with silicon (Si) solar cell with energy gap of 1.124 eV as a tandem solar cell. This tandem approach is an refined solution to improve the efficiency of Si solar cell that has been stuck around 25 % for 15 years. This study focuses on the development of the device configuration model for Si-perovskite tandem solar cell by using SCAPS simulation. The thickness and dopant concentration of perovskite layer have affected the solar cell parameters performance. The efficiency result obtained from SCAPS simulation is 27.29 % for Si-perovskite tandem solar cell with an open circuit voltage of 0.8178 V, short circuit current 43.55 mA/cm2 and fill factor 76.61 %.

  12. Large-scale analysis of tandem repeat variability in the human genome

    PubMed Central

    Duitama, Jorge; Zablotskaya, Alena; Gemayel, Rita; Jansen, An; Belet, Stefanie; Vermeesch, Joris R.; Verstrepen, Kevin J.; Froyen, Guy

    2014-01-01

    Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats can alter the function and/or expression of genes allowing organisms to swiftly adapt to novel environments. Importantly, some repeat expansions have also been linked to certain neurodegenerative diseases. Therefore, accurate sequencing of tandem repeats could contribute to our understanding of common phenotypic variability and might uncover missing genetic factors in idiopathic clinical conditions. However, despite long-standing evidence for the functional role of repeats, they are largely ignored because of technical limitations in sequencing, mapping and typing. Here, we report on a novel capture technique and data filtering protocol that allowed simultaneous sequencing of thousands of tandem repeats in the human genomes of a three generation family using GS-FLX-plus Titanium technology. Our results demonstrated that up to 7.6% of tandem repeats in this family (4% in coding sequences) differ from the reference sequence, and identified a de novo variation in the family tree. The method opens new routes to look at this underappreciated type of genetic variability, including the identification of novel disease-related repeats. PMID:24682812

  13. Advanced astigmatism-corrected tandem Wadsworth mounting for small-scale spectral broadband imaging spectrometer.

    PubMed

    Lei, Yu; Lin, Guan-yu

    2013-01-01

    Tandem gratings of double-dispersion mount make it possible to design an imaging spectrometer for the weak light observation with high spatial resolution, high spectral resolution, and high optical transmission efficiency. The traditional tandem Wadsworth mounting is originally designed to match the coaxial telescope and large-scale imaging spectrometer. When it is used to connect the off-axis telescope such as off-axis parabolic mirror, it presents lower imaging quality than to connect the coaxial telescope. It may also introduce interference among the detector and the optical elements as it is applied to the short focal length and small-scale spectrometer in a close volume by satellite. An advanced tandem Wadsworth mounting has been investigated to deal with the situation. The Wadsworth astigmatism-corrected mounting condition for which is expressed as the distance between the second concave grating and the imaging plane is calculated. Then the optimum arrangement for the first plane grating and the second concave grating, which make the anterior Wadsworth condition fulfilling each wavelength, is analyzed by the geometric and first order differential calculation. These two arrangements comprise the advanced Wadsworth mounting condition. The spectral resolution has also been calculated by these conditions. An example designed by the optimum theory proves that the advanced tandem Wadsworth mounting performs excellently in spectral broadband.

  14. Organic Tandem Solar Cells: Design and Formation

    NASA Astrophysics Data System (ADS)

    Chen, Chun-Chao

    In the past decade, research on organic solar cells has gone through an important development stage leading to major enhancements in power conversion efficiency, from 4% to 9% in single-junction devices. During this period, there are many novel processing techniques and device designs that have been proposed and adapted in organic solar-cell devices. One well-known device architecture that helps maximize the solar cell efficiency is the multi-junction tandem solar-cell design. Given this design, multiple photoactive absorbers as subcells are stacked in a monolithic fashion and assembled via series connection into one complete device, known as the tandem solar cell. Since multiple absorbers with different optical energy bandgaps are being applied in one tandem solar-cell device, the corresponding solar cell efficiency is maximized through expanded absorption spectrum and reduced carrier thermalization loss. In Chapter 3, the architecture of solution-processible, visibly transparent solar cells is introduced. Unlike conventional organic solar-cell devices with opaque electrodes (such as silver, aluminum, gold and etc.), the semi-transparent solar cells rely on highly transparent electrodes and visibly transparent photoactive absorbers. Given these two criteria, we first demonstrated the visibly transparent single-junction solar cells via the polymer absorber with near-infrared absorption and the top electrode based on solution-processible silver nanowire conductor. The highest visible transparency (400 ˜ 700 nm) of 65% was achieved for the complete device structure. More importantly, power conversion efficiency of 4% was also demonstrated. In Chapter 4, we stacked two semi-transparent photoactive absorbers in the tandem architecture in order to realize the semi-transparent tandem solar cells. A noticeable performance improvement from 4% to 7% was observed. More importantly, we modified the interconnecting layers with the incorporation of a thin conjugated

  15. Note on Hovering Turns with Tandem Helicopters

    NASA Technical Reports Server (NTRS)

    Reeder, John P; Tapscott, Robert J

    1955-01-01

    The source of an appreciable pitching-moment difference between left and right hovering turns for a tandem helicopter is described. The difference in pitching moment results from the difference in rotational speed of the counter rotating rotors with respect to the air while the helicopter is turning.

  16. Tandem mirror next step conceptual design

    SciTech Connect

    Doggett, J.N.; Damm, C.C.; Bulmer, R.H.

    1980-10-14

    A study was made to define the features of the experimental mirror fusion device - The Tandem Mirror Next Step, or TMNS - that will bridge the gap between present mirror confinement experiments and a power-producing reactor. We outline the project goals, describe some initial device parameters, and relate the technological requirements to ongoing development programs.

  17. Electrospray tandem mass spectrometric investigations of morphinans.

    PubMed

    Raith, Klaus; Neubert, Reinhard; Poeaknapo, Chotima; Boettcher, Christian; Zenk, Meinhart H; Schmidt, Jürgen

    2003-11-01

    In this study positive ESI tandem mass spectra of the [M + H]+ ions of morphinan alkaloids obtained using an ion trap MS were compared with those from a triple quadrupole MS. This allows to assess the differences of the tandem-in-time versus the tandem-in-space principle, often hampering the development of ESI MS/MS libraries. Fragmentation pathways and possible fragment ion structures were discussed. In order to obtain elemental composition, accurate mass measurements were performed. According to the MS/MS fragmentation pathway, the investigated compounds can be grouped into 4 subsets: (1) morphine and codeine, (2) morphinone, codeinone, and neopinone, (3) thebaine and oripavine, (4) salutaridine and salutaridinol. Salutaridinol-7-O-acetate shows a different fragmentation behavior because of the favored loss of acetic acid. Although most fragment ions occur in both ion trap and triple quad tandem mass spectra, some are exclusively seen in either type. For triple quad, quadrupole time-of-flight and FT-ICR MS/MS, the base peak of morphine results from an ion at m/z 165 that contains neither nitrogen nor oxygen. This ion is not found in ion trap MS/MS, but in subsequential MS3 and MS4.

  18. Technology for large tandem mirror experiments

    SciTech Connect

    Thomassen, K.I.

    1980-09-04

    Construction of a large tandem mirror (MFTF-B) will soon begin at Lawrence Livermore National Laboratory (LLNL). Designed to reach break-even plasma conditions, the facility will significantly advance the physics and technology of magnetic-mirror-based fusion reactors. This paper describes the objectives and the design of the facility.

  19. Modelling of tandem cell temperature coefficients

    SciTech Connect

    Friedman, D.J.

    1996-05-01

    This paper discusses the temperature dependence of the basic solar-cell operating parameters for a GaInP/GaAs series-connected two-terminal tandem cell. The effects of series resistance and of different incident solar spectra are also discussed.

  20. Vortex interaction between two tandem flexible propulsors

    NASA Astrophysics Data System (ADS)

    Park, Sung Goon; Sung, Hyung Jin; Flow Control Laboratory Team

    2015-11-01

    Schooling behaviors of flying and swimming animals are widespread phenomena in nature. Inspired by schooling behaviors of swimming jellyfish, self-propelling flexible bodies with a paddling-based locomotion were modeled in a tandem configuration. The interactions between surrounding fluids and propulsors were considered by using the immersed boundary method. The hydrodynamic patterns generated by the interactions between tandem flexible propulsors were analyzed in the presen study. As a result of the flow-mediated interactions between them, stable configurations were formed spontaneously in which the gap distance between propulsors increased and decreased during the contraction and relaxation phases of the upstream propulsor. The stable configuration was not affected by the initial gap distance but influenced by the phase difference in the flapping frequency between them. Both tandem propulsors benefited from the tandem configuration in terms of the locomotion as compared with an isolated propulsor. This study was supported by the Creative Research Initiatives (No. 2015-001828) program of the National Research Foundation of Korea (MSIP).

  1. 25 MV tandem accelerator at Oak Ridge

    SciTech Connect

    Jones, C.M.

    1980-01-01

    A new heavy-ion accelerator facility is under construction at the Oak Ridge National Laboratory. A brief description of the scope and status of this project is presented with emphasis on the first operational experience with the 25 MV tandem accelerator.

  2. Inverted Three-Junction Tandem Thermophotovoltaic Modules

    NASA Technical Reports Server (NTRS)

    Wojtczuk, Steven

    2012-01-01

    An InGaAs-based three-junction (3J) tandem thermophotovoltaic (TPV) cell has been investigated to utilize more of the blackbody spectrum (from a 1,100 C general purpose heat source GPHS) efficiently. The tandem consists of three vertically stacked subcells, a 0.74-eV InGaAs cell, a 0.6- eV InGaAs cell, and a 0.55-eV InGaAs cell, as well as two interconnecting tunnel junctions. A greater than 20% TPV system efficiency was achieved by another group with a 1,040 C blackbody using a single-bandgap 0.6- eV InGaAs cell MIM (monolithic interconnected module) (30 lateral junctions) that delivered about 12 V/30 or 0.4 V/junction. It is expected that a three-bandgap tandem MIM will eventually have about 3 this voltage (1.15 V) and about half the current. A 4 A/cm2 would be generated by a single-bandgap 0.6-V InGaAs MIM, as opposed to the 2 A/cm2 available from the same spectrum when split among the three series-connected junctions in the tandem stack. This would then be about a 50% increase (3xVoc, 0.5xIsc) in output power if the proposed tandem replaced the single- bandgap MIM. The advantage of the innovation, if successful, would be a 50% increase in power conversion efficiency from radioisotope heat sources using existing thermophotovoltaics. Up to 50% more power would be generated for radioisotope GPHS deep space missions. This type of InGaAs multijunction stack could be used with terrestrial concentrator solar cells to increase efficiency from 41 to 45% or more.

  3. Quality evaluation of tandem mass spectral libraries.

    PubMed

    Oberacher, Herbert; Weinmann, Wolfgang; Dresen, Sebastian

    2011-06-01

    Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

  4. Numerical modeling of GaInP/GaAs monolithic tandem solar cells

    NASA Astrophysics Data System (ADS)

    Mahfoud, Abderrezak; Fathi, Mohamed; Belghachi, Abderrahmane; Djahli, Farid

    2016-07-01

    In this work, we present simulation of a monolithic tandem GaInP/GaAs solar cell made from a top GaInP cell and a bottom GaAs cell. For this purpose we used one dimensional simulation program tool called Solar Cell Capacitance Simulator in one Dimension (SCAPS-1D), the proposed methodology consists of simulating each cell separately. For enhanced electric characteristics of a tandem solar cell, the current-match condition between the top and bottom cells should be satisfied, which in turn requires careful design of the tandem parameters. To fulfill this condition, the top cell base thickness of (GaInP) is adjusted accordingly. The solar spectrum reaching the lower cell is computed by subtracting the top cell spectrum from the total solar spectrum. The optimal value of the short circuit current density corresponds to a top cell's base thickness of 0.7 μm; this results in an open circuit voltage of 2.397 V, a short circuit current density of 13.87 mA/cm2, an efficiency of 29.83 % and a fill factor of 89.74 % under the AM1.5G solar spectrum.

  5. Porous SiO₂/MgF₂ broadband antireflection coatings for superstrate-type silicon-based tandem cells.

    PubMed

    Wang, Na-Fu; Kuo, Ting-Wei; Tsai, Yu-Zen; Lin, Shi-Xiong; Hung, Pin-Kun; Lin, Chiung-Lin; Houng, Mau-Phon

    2012-03-26

    The purpose of this study is to reduce the glass substrate reflectivity over a wide spectral range (400-1200 nm) without having high reflectivity in the near-infrared region. After making porous SiO₂/MgF₂ double-layer antireflection (DLAR) thin film structure, the superstrate-type silicon-based tandem cells are added. In comparison to having only silicon-based tandem solar cells, the short-circuit current density has improved by 6.82% when porous SiO₂/MgF₂ DLAR thin film is applied to silicon-based tandem solar cells. This study has demonstrated that porous SiO₂/MgF₂ DLAR thin film structure provides antireflection properties over a broad spectral range (400-1200 nm) without having high reflectivity at near-infrared wavelengths.

  6. Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains: Implications for Actin Filament Nucleation

    SciTech Connect

    Rebowski, Grzegorz; Namgoong, Suk; Boczkowska, Malgorzata; Leavis, Paul C.; Navaza, Jorge; Dominguez, Roberto

    2013-11-20

    Actin filament nucleators initiate polymerization in cells in a regulated manner. A common architecture among these molecules consists of tandem WASP homology 2 domains (W domains) that recruit three to four actin subunits to form a polymerization nucleus. We describe a low-resolution crystal structure of an actin dimer assembled by tandem W domains, where the first W domain is cross-linked to Cys374 of the actin subunit bound to it, whereas the last W domain is followed by the C-terminal pointed end-capping helix of thymosin {beta}4. While the arrangement of actin subunits in the dimer resembles that of a long-pitch helix of the actin filament, important differences are observed. These differences result from steric hindrance of the W domain with intersubunit contacts in the actin filament. We also determined the structure of the first W domain of Vibrio parahaemolyticus VopL cross-linked to actin Cys374 and show it to be nearly identical with non-cross-linked W-Actin structures. This result validates the use of cross-linking as a tool for the study of actin nucleation complexes, whose natural tendency to polymerize interferes with most structural methods. Combined with a biochemical analysis of nucleation, the structures may explain why nucleators based on tandem W domains with short inter-W linkers have relatively weak activity, cannot stay bound to filaments after nucleation, and are unlikely to influence filament elongation. The findings may also explain why nucleation-promoting factors of the Arp2/3 complex, which are related to tandem-W-domain nucleators, are ejected from branch junctions after nucleation. We finally show that the simple addition of the C-terminal pointed end-capping helix of thymosin {beta}4 to tandem W domains can change their activity from actin filament nucleation to monomer sequestration.

  7. Structure of a longitudinal actin dimer assembled by tandem w domains: implications for actin filament nucleation.

    PubMed

    Rebowski, Grzegorz; Namgoong, Suk; Boczkowska, Malgorzata; Leavis, Paul C; Navaza, Jorge; Dominguez, Roberto

    2010-10-15

    Actin filament nucleators initiate polymerization in cells in a regulated manner. A common architecture among these molecules consists of tandem WASP homology 2 domains (W domains) that recruit three to four actin subunits to form a polymerization nucleus. We describe a low-resolution crystal structure of an actin dimer assembled by tandem W domains, where the first W domain is cross-linked to Cys374 of the actin subunit bound to it, whereas the last W domain is followed by the C-terminal pointed end-capping helix of thymosin β4. While the arrangement of actin subunits in the dimer resembles that of a long-pitch helix of the actin filament, important differences are observed. These differences result from steric hindrance of the W domain with intersubunit contacts in the actin filament. We also determined the structure of the first W domain of Vibrio parahaemolyticus VopL cross-linked to actin Cys374 and show it to be nearly identical with non-cross-linked W-Actin structures. This result validates the use of cross-linking as a tool for the study of actin nucleation complexes, whose natural tendency to polymerize interferes with most structural methods. Combined with a biochemical analysis of nucleation, the structures may explain why nucleators based on tandem W domains with short inter-W linkers have relatively weak activity, cannot stay bound to filaments after nucleation, and are unlikely to influence filament elongation. The findings may also explain why nucleation-promoting factors of the Arp2/3 complex, which are related to tandem-W-domain nucleators, are ejected from branch junctions after nucleation. We finally show that the simple addition of the C-terminal pointed end-capping helix of thymosin β4 to tandem W domains can change their activity from actin filament nucleation to monomer sequestration.

  8. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria.

    PubMed

    Lindstedt, Bjørn-Arne

    2005-06-01

    DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.

  9. Tandem repeats and length variation in the mitochondrial DNA control region of Epirrita autumnata (Lepidoptera: Geometridae).

    PubMed

    Snäll, N; Huoponen, K; Savontaus, M L; Ruohomäki, K

    2002-10-01

    The organization of the mitochondrial DNA (mtDNA) control region (CR) of the autumnal moth, Epirrita autumnata, is described. The E. autumnata CR presents a distinct type of lepidopteran CR with domains of non-repetitive and repetitive sequences. The CRs show considerable length variation owing to a variable number of short approximately 29-bp sequence blocks that are repeated between 6 and 14 times in tandem. The organization of such a tandem array is unique among the insect CRs examined so far. Furthermore, the E. autumnata CR, which may reach 1075 bp in length, is considerably longer than previously reported lepidopteran CRs, which reach 311-499 bp in length. Like other lepidopteran CRs, the E. autumnata CR contains two long homopolymer runs that may be involved in mtDNA replication and (or) transcription.

  10. Tandem microwave waste remediation and decontamination system

    DOEpatents

    Wicks, George G.; Clark, David E.; Schulz, Rebecca L.

    1999-01-01

    The invention discloses a tandem microwave system consisting of a primary chamber in which microwave energy is used for the controlled combustion of materials. A second chamber is used to further treat the off-gases from the primary chamber by passage through a susceptor matrix subjected to additional microwave energy. The direct microwave radiation and elevated temperatures provide for significant reductions in the qualitative and quantitative emissions of the treated off gases. The tandem microwave system can be utilized for disinfecting wastes, sterilizing materials, and/or modifying the form of wastes to solidify organic or inorganic materials. The simple design allows on-site treatment of waste by small volume waste generators.

  11. Progress in the tandem mirror program

    NASA Astrophysics Data System (ADS)

    Fowler, T. K.; Borchers, R. R.

    1981-09-01

    Experimental results in TMX have confirmed the basic principles of the tandem mirror concept. A center cell particle confinement parameter eta tau approximately one hundred billion cu cm obtained at ion temperatures around 100 eV, which is a hundred fold improvement over single mirrors at the same temperatures. For TMX these results were obtained at peak beta values in the center cell in the range 10 to 40%, not yet limited by MHD activity, and ion cyclotron resonant heating in the Phaedrus tandem mirror experiment has produced beta values approximately 25%, which is several times the ideal MHD limit for that device. In addition, it was demonstrated that the end fan chambers of TMX simultaneously isolate the hot electrons from the end walls, provide adequate pumping and conveniently dispose of the exhaust plasma energy either by thermal deposition on the end wall or by direct conversion to electricity (at 48% efficiency in agreement with calculations).

  12. Mechanically stacked concentrator tandem solar cells

    NASA Technical Reports Server (NTRS)

    Andreev, V. M.; Rumyantsev, V. D.; Karlina, L. B.; Kazantsev, A. B.; Khvostikov, V. P.; Shvarts, M. Z.; Sorokina, S. V.

    1995-01-01

    Four-terminal mechanically stacked solar cells were developed for advanced space arrays with line-focus reflective concentrators. The top cells are based on AlGaAs/GaAs multilayer heterostructures prepared by low temperature liquid phase epitaxy. The bottom cells are based on heteroepitaxial InP/InGaAs liquid phase epitaxy or on homo-junction GaSb, Zn-diffused structures. The sum of the highest reached efficiencies of the top and bottom cells is 29.4 percent. The best four-terminal tandems have an efficiency of 27 to 28 percent. Solar cells were irradiated with 1 MeV electrons and their performances were determined as a function of fluence up to 10(exp 16) cm(exp-2). It was shown that the radiation resistance of developed tandem cells is similar to the most radiative stable AlGaAs/GaAs cells with a thin p-GaAs photoactive layer.

  13. Current results of the tandem mirror experiment

    SciTech Connect

    Drake, R.P.

    1980-04-09

    The basic operating characteristics of the Tandem Mirror Experiment, (TMX) at the Lawrence Livermore Laboratory in the USA have been established. Tandem-mirror plasmas have been produced using neutral-beam-fueled end plugs and a gas-fueled center cell. An axial potential well between the end plugs has been measured. There is direct evidence that this potential well enhances the axial confinement of the center-cell ions. The observed densities and loss currents are consistent with preliminary studies of the particle sources and losses near the magnetic axis. The observed confinement is consistent with theory when plasma fluctuations are low. When the requirement of drift-cyclotron loss-cone mode stability is violated, the plasma fluctuations degrade the center-cell confinement.

  14. The LLNL multi-user tandem laboratory

    NASA Astrophysics Data System (ADS)

    Davis, J. C.

    1989-04-01

    An FN tandem laboratory, cofunded by several Lawrence Livermore National Laboratory Divisions, Sandia Livermore, and the University of California Regents, is now operational at Livermore. The accelerator, formerly the University of Washington injector, has been upgraded with SF 6, Dowlish tubes, and a NEC pelletron charging system. A conventional duoplasmatron, a tritium source, and two Cs sputtering sources will be fielded on the accelerator. Pulsed beams will be available from two source positions. The laboratory has been designed to accommodate up to 19 experimental positions with excellent optics and working vacuum. The facility is unshielded with both accelerator and radiological systems under the control of a distributed microprocessor system. Research activities at the tandem include nuclear physics and astrophysics, materials science and characterization programs, and accelerator mass spectrometry for archaeology, biomedical, environmental and geoscience investigators.

  15. Locomotion by Tandem and Parallel Wings

    NASA Astrophysics Data System (ADS)

    Tanida, Yoshimichi

    A two-dimensional analysis was carried out on the locomotion by tandem and parallel wings in relation to the free flight of dragonflies and beetles, remarking the mutual interference between fore and hind wings. The results obtained are summarized as follows: In the case of tandem wings, (1)High thrust and propulsive efficiency can be achieved when the forewing oscillates with a definite phase lag behind the hindwing, as in the case of real dragonflies, (2)Somewhat smaller amplitude of hindwing leads to optimum condition for work sharing of two wings, (3)The hard forewing does not serve for the thrust and propulsive efficiency, whereas the hard hindwing does for the augmentation of them; In the case of parallel wings, (4)The hard wing placed near the soft wing acts nearly as an infinite plate, as for the ground effect, increasing both thrust and propulsive efficiency.

  16. Steroid Hormone Analysis by Tandem Mass Spectrometry

    PubMed Central

    Soldin, Steven J.; Soldin, Offie P.

    2013-01-01

    BACKGROUND New high-performance liquid chromatography/ tandem mass spectrometry (LC-MS/MS) methods are among the most successful approaches to improve specificity problems inherent in many immunoassays. CONTENT We emphasize problems with immunoassays for the measurement of steroids and review the emerging role of LC-MS/MS in the measurement of clinically relevant steroids. The latest generation of tandem mass spectrometers has superior limits of quantification, permitting omission of previously employed derivatization steps. The measurement of steroid profiles in the diagnosis and treatment of congenital adrenal hyperplasia, adrenal insufficiency, chronic pelvic pain and prostatitis, oncology (breast cancer), and athletes has important new applications. CONCLUSIONS LC-MS/MS now affords the specificity, imprecision, and limits of quantification necessary for the reliable measurement of steroids in human fluids, enhancing diagnostic capabilities, particularly when steroid profiles are available. PMID:19325015

  17. DDES and IDDES of tandem cylinders.

    SciTech Connect

    Balakrishnan, R.; Garbaruk, A.; Shur, M.; Strelets, M.; Spalart, P.; New Technologies and Services - Russia; St.-Peterburg State Polytechnic Univ.; Boeing Commercial Airplanes

    2010-09-09

    The paper presents an overview of the authors contribution to the BANC-I Workshop on the flow past tandem cylinders (Category 2). It includes an outline of the simulation approaches, numerics, and grid used, the major results of the simulations, their comparison with available experimental data, and some preliminary conclusions. The effect of varying the spanwise period in the simulations is strong for some quantities, and not others.

  18. Cold Climate Heat Pumps Using Tandem Compressors

    SciTech Connect

    Shen, Bo; Abdelaziz, Omar; Rice, C Keith; Baxter, Van D

    2016-01-01

    In cold climate zones, e.g. ASHRAE climate regions IV and V, conventional electric air-source heat pumps (ASHP) do not work well, due to high compressor discharge temperatures, large pressure ratios and inadequate heating capacities at low ambient temperatures. Consequently, significant use of auxiliary strip heating is required to meet the building heating load. We introduce innovative ASHP technologies as part of continuing efforts to eliminate auxiliary strip heat use and maximize heating COP with acceptable cost-effectiveness and reliability. These innovative ASHP were developed using tandem compressors, which are capable of augmenting heating capacity at low temperatures and maintain superior part-load operation efficiency at moderate temperatures. Two options of tandem compressors were studied; the first employs two identical, single-speed compressors, and the second employs two identical, vapor-injection compressors. The investigations were based on system modeling and laboratory evaluation. Both designs have successfully met the performance criteria. Laboratory evaluation showed that the tandem, single-speed compressor ASHP system is able to achieve heating COP = 4.2 at 47 F (8.3 C), COP = 2.9 at 17 F (-8.3 C), and 76% rated capacity and COP = 1.9 at -13 F (-25 C). This yields a HSPF = 11.0 (per AHRI 210/240). The tandem, vapor-injection ASHP is able to reach heating COP = 4.4 at 47 F, COP = 3.1 at 17 F, and 88% rated capacity and COP = 2.0 at -13 F. This yields a HSPF = 12.0. The system modeling and further laboratory evaluation are presented in the paper.

  19. Current and lattice matched tandem solar cell

    DOEpatents

    Olson, Jerry M.

    1987-01-01

    A multijunction (cascade) tandem photovoltaic solar cell device is fabricated of a Ga.sub.x In.sub.1-x P (0.505.ltoreq.X.ltoreq.0.515) top cell semiconductor lattice matched to a GaAs bottom cell semiconductor at a low-resistance heterojunction, preferably a p+/n+ heterojunction between the cells. The top and bottom cells are both lattice matched and current matched for high efficiency solar radiation conversion to electrical energy.

  20. Oak Ridge 25-MV tandem accelerator

    SciTech Connect

    Ziegler, N.F.; Richardson, E.G.; Mann, J.E.; Juras, R.C.; Jones, C.M.; Biggerstaff, J.A.; Benjamin, J.A.

    1981-01-01

    A new heavy-ion accelerator facility is nearing completion at the Oak Ridge National Laboratory. This paper presents a brief description of the scope and status of this project and a discussion of some aspects of the first operational experience with the 25 MV tandem accelerator which is being provided by the National Electrostatics Corporation (NEC) as a major component of the first phase of the facility.

  1. Flow field interactions between two tandem cyclists

    NASA Astrophysics Data System (ADS)

    Barry, Nathan; Burton, David; Sheridan, John; Thompson, Mark; Brown, Nicholas A. T.

    2016-12-01

    Aerodynamic drag is the primary resistive force acting on cyclists at racing speeds. Many events involve cyclists travelling in very close proximity. Previous studies have shown that interactions result in significant drag reductions for inline cyclists. However, the interaction between cyclist leg position (pedalling) and the vortical flow structures that contribute significantly to the drag on an isolated cyclist has not previously been quantified or described for tandem cyclists of varying separation. To this end, scale model cyclists were constructed for testing in a water channel for inline tandem configurations. Particle image velocimetry was used to capture time-averaged velocity fields around two tandem cyclists. Perhaps surprisingly, the wake of a trailing cyclist maintains strong similarity to the characteristic wake of a single cyclist despite a significant disturbance to the upstream flow. Together with streamwise velocity measurements through the wake and upstream of the trailing cyclist, this work supports previous findings, which showed that the trailing cyclist drag reduction is primarily due to upstream sheltering effects reducing the stagnation pressure on forward-facing surfaces.

  2. TandEM: Titan and Enceladus mission

    NASA Astrophysics Data System (ADS)

    Coustenis, A.; Atreya, S. K.; Balint, T.; Brown, R. H.; Dougherty, M. K.; Ferri, F.; Fulchignoni, M.; Gautier, D.; Gowen, R. A.; Griffith, C. A.; Gurvits, L. I.; Jaumann, R.; Langevin, Y.; Leese, M. R.; Lunine, J. I.; McKay, C. P.; Moussas, X.; Müller-Wodarg, I.; Neubauer, F.; Owen, T. C.; Raulin, F.; Sittler, E. C.; Sohl, F.; Sotin, C.; Tobie, G.; Tokano, T.; Turtle, E. P.; Wahlund, J.-E.; Waite, J. H.; Baines, K. H.; Blamont, J.; Coates, A. J.; Dandouras, I.; Krimigis, T.; Lellouch, E.; Lorenz, R. D.; Morse, A.; Porco, C. C.; Hirtzig, M.; Saur, J.; Spilker, T.; Zarnecki, J. C.; Choi, E.; Achilleos, N.; Amils, R.; Annan, P.; Atkinson, D. H.; Bénilan, Y.; Bertucci, C.; Bézard, B.; Bjoraker, G. L.; Blanc, M.; Boireau, L.; Bouman, J.; Cabane, M.; Capria, M. T.; Chassefière, E.; Coll, P.; Combes, M.; Cooper, J. F.; Coradini, A.; Crary, F.; Cravens, T.; Daglis, I. A.; de Angelis, E.; de Bergh, C.; de Pater, I.; Dunford, C.; Durry, G.; Dutuit, O.; Fairbrother, D.; Flasar, F. M.; Fortes, A. D.; Frampton, R.; Fujimoto, M.; Galand, M.; Grasset, O.; Grott, M.; Haltigin, T.; Herique, A.; Hersant, F.; Hussmann, H.; Ip, W.; Johnson, R.; Kallio, E.; Kempf, S.; Knapmeyer, M.; Kofman, W.; Koop, R.; Kostiuk, T.; Krupp, N.; Küppers, M.; Lammer, H.; Lara, L.-M.; Lavvas, P.; Le Mouélic, S.; Lebonnois, S.; Ledvina, S.; Li, J.; Livengood, T. A.; Lopes, R. M.; Lopez-Moreno, J.-J.; Luz, D.; Mahaffy, P. R.; Mall, U.; Martinez-Frias, J.; Marty, B.; McCord, T.; Menor Salvan, C.; Milillo, A.; Mitchell, D. G.; Modolo, R.; Mousis, O.; Nakamura, M.; Neish, C. D.; Nixon, C. A.; Nna Mvondo, D.; Orton, G.; Paetzold, M.; Pitman, J.; Pogrebenko, S.; Pollard, W.; Prieto-Ballesteros, O.; Rannou, P.; Reh, K.; Richter, L.; Robb, F. T.; Rodrigo, R.; Rodriguez, S.; Romani, P.; Ruiz Bermejo, M.; Sarris, E. T.; Schenk, P.; Schmitt, B.; Schmitz, N.; Schulze-Makuch, D.; Schwingenschuh, K.; Selig, A.; Sicardy, B.; Soderblom, L.; Spilker, L. J.; Stam, D.; Steele, A.; Stephan, K.; Strobel, D. F.; Szego, K.; Szopa, C.; Thissen, R.; Tomasko, M. G.; Toublanc, D.; Vali, H.; Vardavas, I.; Vuitton, V.; West, R. A.; Yelle, R.; Young, E. F.

    2009-03-01

    TandEM was proposed as an L-class (large) mission in response to ESA’s Cosmic Vision 2015-2025 Call, and accepted for further studies, with the goal of exploring Titan and Enceladus. The mission concept is to perform in situ investigations of two worlds tied together by location and properties, whose remarkable natures have been partly revealed by the ongoing Cassini-Huygens mission. These bodies still hold mysteries requiring a complete exploration using a variety of vehicles and instruments. TandEM is an ambitious mission because its targets are two of the most exciting and challenging bodies in the Solar System. It is designed to build on but exceed the scientific and technological accomplishments of the Cassini-Huygens mission, exploring Titan and Enceladus in ways that are not currently possible (full close-up and in situ coverage over long periods of time). In the current mission architecture, TandEM proposes to deliver two medium-sized spacecraft to the Saturnian system. One spacecraft would be an orbiter with a large host of instruments which would perform several Enceladus flybys and deliver penetrators to its surface before going into a dedicated orbit around Titan alone, while the other spacecraft would carry the Titan in situ investigation components, i.e. a hot-air balloon (Montgolfière) and possibly several landing probes to be delivered through the atmosphere.

  3. TandEM: Titan and Enceladus mission

    USGS Publications Warehouse

    Coustenis, A.; Atreya, S.K.; Balint, T.; Brown, R.H.; Dougherty, M.K.; Ferri, F.; Fulchignoni, M.; Gautier, D.; Gowen, R.A.; Griffith, C.A.; Gurvits, L.I.; Jaumann, R.; Langevin, Y.; Leese, M.R.; Lunine, J.I.; McKay, C.P.; Moussas, X.; Muller-Wodarg, I.; Neubauer, F.; Owen, T.C.; Raulin, F.; Sittler, E.C.; Sohl, F.; Sotin, Christophe; Tobie, G.; Tokano, T.; Turtle, E.P.; Wahlund, J.-E.; Waite, J.H.; Baines, K.H.; Blamont, J.; Coates, A.J.; Dandouras, I.; Krimigis, T.; Lellouch, E.; Lorenz, R.D.; Morse, A.; Porco, C.C.; Hirtzig, M.; Saur, J.; Spilker, T.; Zarnecki, J.C.; Choi, E.; Achilleos, N.; Amils, R.; Annan, P.; Atkinson, D.H.; Benilan, Y.; Bertucci, C.; Bezard, B.; Bjoraker, G.L.; Blanc, M.; Boireau, L.; Bouman, J.; Cabane, M.; Capria, M.T.; Chassefiere, E.; Coll, P.; Combes, M.; Cooper, J.F.; Coradini, A.; Crary, F.; Cravens, T.; Daglis, I.A.; de Angelis, E.; De Bergh, C.; de Pater, I.; Dunford, C.; Durry, G.; Dutuit, O.; Fairbrother, D.; Flasar, F.M.; Fortes, A.D.; Frampton, R.; Fujimoto, M.; Galand, M.; Grasset, O.; Grott, M.; Haltigin, T.; Herique, A.; Hersant, F.; Hussmann, H.; Ip, W.; Johnson, R.; Kallio, E.; Kempf, S.; Knapmeyer, M.; Kofman, W.; Koop, R.; Kostiuk, T.; Krupp, N.; Kuppers, M.; Lammer, H.; Lara, L.-M.; Lavvas, P.; Le, Mouelic S.; Lebonnois, S.; Ledvina, S.; Li, Ji; Livengood, T.A.; Lopes, R.M.; Lopez-Moreno, J. -J.; Luz, D.; Mahaffy, P.R.; Mall, U.; Martinez-Frias, J.; Marty, B.; McCord, T.; Salvan, C.M.; Milillo, A.; Mitchell, D.G.; Modolo, R.; Mousis, O.; Nakamura, M.; Neish, Catherine D.; Nixon, C.A.; Mvondo, D.N.; Orton, G.; Paetzold, M.; Pitman, J.; Pogrebenko, S.; Pollard, W.; Prieto-Ballesteros, O.; Rannou, P.; Reh, K.; Richter, L.; Robb, F.T.; Rodrigo, R.; Rodriguez, S.; Romani, P.; Bermejo, M.R.; Sarris, E.T.; Schenk, P.; Schmitt, B.; Schmitz, N.; Schulze-Makuch, D.; Schwingenschuh, K.; Selig, A.; Sicardy, B.; Soderblom, L.; Spilker, L.J.; Stam, D.; Steele, A.; Stephan, K.; Strobel, D.F.; Szego, K.; Szopa,

    2009-01-01

    TandEM was proposed as an L-class (large) mission in response to ESA's Cosmic Vision 2015-2025 Call, and accepted for further studies, with the goal of exploring Titan and Enceladus. The mission concept is to perform in situ investigations of two worlds tied together by location and properties, whose remarkable natures have been partly revealed by the ongoing Cassini-Huygens mission. These bodies still hold mysteries requiring a complete exploration using a variety of vehicles and instruments. TandEM is an ambitious mission because its targets are two of the most exciting and challenging bodies in the Solar System. It is designed to build on but exceed the scientific and technological accomplishments of the Cassini-Huygens mission, exploring Titan and Enceladus in ways that are not currently possible (full close-up and in situ coverage over long periods of time). In the current mission architecture, TandEM proposes to deliver two medium-sized spacecraft to the Saturnian system. One spacecraft would be an orbiter with a large host of instruments which would perform several Enceladus flybys and deliver penetrators to its surface before going into a dedicated orbit around Titan alone, while the other spacecraft would carry the Titan in situ investigation components, i.e. a hot-air balloon (Montgolfi??re) and possibly several landing probes to be delivered through the atmosphere. ?? Springer Science + Business Media B.V. 2008.

  4. Organic Light-Emitting Devices with Tandem Structure.

    PubMed

    Chiba, Takayuki; Pu, Yong-Jin; Kido, Junji

    2016-06-01

    Tandem organic light-emitting devices (OLEDs) have attracted considerable attention for solid-state lighting and flat panel displays because their tandem architecture enables high efficiency and long operational lifetime simultaneously. In the tandem OLED structure, plural light-emitting units (LEUs) are stacked in series through a charge generation layer (CGL) and an electron injection layer (EIL). In this chapter, we focus on the key features of tandem OLEDs for high efficiency and long operational lifetimes. We also demonstrate the effect of the CGL comprising a Lewis acid, an n-type semiconductor metal oxide, and an organic electron-accepting material. We discuss the two types of EILs in tandem OLEDs: alkali metals containing n-type compounds and ultra-thin metals. Finally, we focus on the recent progress of the state-of-the-art solution-processed tandem OLEDs.

  5. Status of the JAERI tandem accelerator and its booster

    SciTech Connect

    Takeuchi, Suehiro; Abe, Shinichi; Hanashima, Susumu; Horie, Katsuzo; Ishizaki, Nobuhiro; Kanda, Susumu; Matsuda, Makoto; Ohuchi, Isao; Tayama, Hidekazu; Tsukihashi, Yoshihiro; Yoshida, Tadashi

    1999-04-26

    The JAERI tandem accelerator has been operating effectively since 1982 and heavy ions from the tandem has been boosted in energy by the superconducting independently phased booster linac for the experiments at higher bombarding energies since 1994. Present operating status of the tandem accelerator and its booster, status of their use for experiments and an on-going improvement project with an ECR ion source are described.

  6. Flexible and fragmentable tandem photosensitive nanocrystal skins

    NASA Astrophysics Data System (ADS)

    Akhavan, S.; Uran, C.; Bozok, B.; Gungor, K.; Kelestemur, Y.; Lesnyak, V.; Gaponik, N.; Eychmüller, A.; Demir, H. V.

    2016-02-01

    We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of single monolayers of colloidal water-soluble CdTe and CdHgTe nanocrystals (NCs) in adjacent junctions on a Kapton polymer tape. Owing to the usage of a single NC layer in each junction, noise generation was significantly reduced while keeping the resulting PNS films considerably transparent. In each junction, photogenerated excitons are dissociated at the interface of the semi-transparent Al electrode and the NC layer, with holes migrating to the contact electrode and electrons trapped in the NCs. As a result, the tandem PNSs lead to an open-circuit photovoltage buildup equal to the sum of those of the two single junctions, exhibiting a total voltage buildup of 128.4 mV at an excitation intensity of 75.8 μW cm-2 at 350 nm. Furthermore, we showed that these flexible PNSs could be bent over 3.5 mm radius of curvature and cut out in arbitrary shapes without damaging the operation of individual parts and without introducing any significant loss in the total sensitivity. These findings indicate that the NC skins are promising as building blocks to make low-cost, flexible, large-area UV/visible sensing platforms with highly efficient full-spectrum conversion.We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of

  7. Flexible and fragmentable tandem photosensitive nanocrystal skins.

    PubMed

    Akhavan, S; Uran, C; Bozok, B; Gungor, K; Kelestemur, Y; Lesnyak, V; Gaponik, N; Eychmüller, A; Demir, H V

    2016-02-28

    We proposed and demonstrated the first account of large-area, semi-transparent, tandem photosensitive nanocrystal skins (PNSs) constructed on flexible substrates operating on the principle of photogenerated potential buildup, which avoid the need for applying an external bias and circumvent the current-matching limitation between junctions. We successfully fabricated and operated the tandem PNSs composed of single monolayers of colloidal water-soluble CdTe and CdHgTe nanocrystals (NCs) in adjacent junctions on a Kapton polymer tape. Owing to the usage of a single NC layer in each junction, noise generation was significantly reduced while keeping the resulting PNS films considerably transparent. In each junction, photogenerated excitons are dissociated at the interface of the semi-transparent Al electrode and the NC layer, with holes migrating to the contact electrode and electrons trapped in the NCs. As a result, the tandem PNSs lead to an open-circuit photovoltage buildup equal to the sum of those of the two single junctions, exhibiting a total voltage buildup of 128.4 mV at an excitation intensity of 75.8 μW cm(-2) at 350 nm. Furthermore, we showed that these flexible PNSs could be bent over 3.5 mm radius of curvature and cut out in arbitrary shapes without damaging the operation of individual parts and without introducing any significant loss in the total sensitivity. These findings indicate that the NC skins are promising as building blocks to make low-cost, flexible, large-area UV/visible sensing platforms with highly efficient full-spectrum conversion.

  8. Effects of practicing tandem gait with and without vibrotactile biofeedback in subjects with unilateral vestibular loss

    PubMed Central

    Dozza, Marco; Wall, Conrad; Peterka, Robert J.; Chiari, Lorenzo; Horak, Fay B.

    2008-01-01

    Subjects with unilateral vestibular loss exhibit motor control impairments as shown by body and limb deviation during gait. Biofeedback devices have been shown to improve stance postural control, especially when sensory information is limited by environmental conditions or pathologies such as unilateral vestibular loss. However, the extent to which biofeedback could improve motor performance or learning while practicing a dynamic task such as narrow gait is still unknown. In this cross-over design study, 9 unilateral vestibular loss subjects practiced narrow gait with and without wearing a trunk-tilt, biofeedback device in 2 practice sessions. The biofeedback device informed the subjects of their medial-lateral angular tilt and tilt velocity during gait via vibration of the trunk. From motion analysis and tilt data, the performance of the subjects practicing tandem gait were compared over time with and without biofeedback. By practicing tandem gait, subjects reduced their trunk-tilt, center of mass displacement, medial-lateral feet distance, and frequency of stepping error. In both groups, use of tactile biofeedback consistently increased postural stability during tandem gait, beyond the effects of practice alone. However, one single session of practice with biofeedback did not result in conclusive short-term after-effects consistent with short-term retention of motor performance without this additional biofeedback. Results from this study support the hypothesis that tactile biofeedback acts similar to natural sensory feedback to improve dynamic motor performance but does not facilitate a recalibration of motor performance to improve function after short-term use. PMID:18525145

  9. Tandem robot control system and method for controlling mobile robots in tandem

    DOEpatents

    Hayward, David R.; Buttz, James H.; Shirey, David L.

    2002-01-01

    A control system for controlling mobile robots provides a way to control mobile robots, connected in tandem with coupling devices, to navigate across difficult terrain or in closed spaces. The mobile robots can be controlled cooperatively as a coupled system in linked mode or controlled individually as separate robots.

  10. 47 CFR 69.111 - Tandem-switched transport and tandem charge.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... where the incumbent local exchange carrier has implemented density pricing zones as described in section... circuits used in the tandem to end office links (or a surrogate based on the proportion of copper and fiber... exchange carrier. (ii) In study areas where the incumbent local exchange carrier has implemented density...

  11. 47 CFR 69.111 - Tandem-switched transport and tandem charge.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... areas where the incumbent local exchange carrier has implemented density pricing zones as described in... circuits used in the tandem to end office links (or a surrogate based on the proportion of copper and fiber... exchange carrier. (ii) In study areas where the incumbent local exchange carrier has implemented density...

  12. The Naples University 3 MV tandem accelerator

    SciTech Connect

    Campajola, L.; Brondi, A.

    2013-07-18

    The 3 MV tandem accelerator of the Naples University is used for research activities and applications in many fields. At the beginning of operation (1977) the main utilization was in the field of nuclear physics. Later, the realization of new beam lines allowed the development of applied activities as radiocarbon dating, ion beam analysis, biophysics, ion implantation etc. At present, the availability of different ion sources and many improvements on the accelerator allow to run experiments in a wide range of subjects. An overview of the characteristics and major activities of the laboratory is presented.

  13. Method of fabricating bifacial tandem solar cells

    SciTech Connect

    Wojtczuk, Steven J; Chiu, Philip T; Zhang, Xuebing; Gagnon, Edward; Timmons, Michael

    2014-10-07

    A method of fabricating on a semiconductor substrate bifacial tandem solar cells with semiconductor subcells having a lower bandgap than the substrate bandgap on one side of the substrate and with subcells having a higher bandgap than the substrate on the other including, first, growing a lower bandgap subcell on one substrate side that uses only the same periodic table group V material in the dislocation-reducing grading layers and bottom subcells as is present in the substrate and after the initial growth is complete and then flipping the substrate and growing the higher bandgap subcells on the opposite substrate side which can be of different group V material.

  14. A Hybrid Approach To Tandem Cylinder Noise

    NASA Technical Reports Server (NTRS)

    Lockard, David P.

    2004-01-01

    Aeolian tone generation from tandem cylinders is predicted using a hybrid approach. A standard computational fluid dynamics (CFD) code is used to compute the unsteady flow around the cylinders, and the acoustics are calculated using the acoustic analogy. The CFD code is nominally second order in space and time and includes several turbulence models, but the SST k - omega model is used for most of the calculations. Significant variation is observed between laminar and turbulent cases, and with changes in the turbulence model. A two-dimensional implementation of the Ffowcs Williams-Hawkings (FW-H) equation is used to predict the far-field noise.

  15. Terminal ion source for an FN tandem

    SciTech Connect

    Harper, G.C.

    1995-09-01

    An RF discharge source assembly has been developed for use in the terminal of the FN tandem van de Graaff accelerator at the Nuclear Physics Laboratory of the University of Washington. The primary motivation for developing the source was to provide a high intensity beam of {sup 3}He{sup +} to produce {sup 8}B from the reaction {sub 6}Li({sup 3}He,n){sup 8}B. The design of the optics and the performance of the source are described here.

  16. Some new ideas for Tandem Mirror blankets

    SciTech Connect

    Neef, W.S. Jr.

    1981-10-12

    The Tandem Mirror Reactor, with its cylindrical central cell, has led to numerous blanket designs taking advantage of the simple geometry. Also many new applications for fusion neutrons are now being considered. To the pure fusion electricity producers and hybrids producing fissile fuel, we are adding studies of synthetic fuel producers and fission-suppressed hybrids. The three blanket concepts presented are new ideas and should be considered illustrative of the breadth of Livermore's application studies. They are not meant to imply fully analyzed designs.

  17. Changes in Variable Number of Tandem Repeats in 'Candidatus Liberibacter asiaticus' through Insect Transmission.

    PubMed

    Katoh, Hiroshi; Inoue, Hiromitsu; Iwanami, Toru

    2015-01-01

    Citrus greening (huanglongbing) is the most destructive citrus disease worldwide. The disease is associated with three species of 'Candidatus Liberibacter' among which 'Ca. Liberibacter asiaticus' has the widest distribution. 'Ca. L. asiaticus' is commonly transmitted by a phloem-feeding insect vector, the Asian citrus psyllid Diaphorina citri. A previous study showed that isolates of 'Ca. L. asiaticus' were clearly differentiated by variable number of tandem repeat (VNTR) profiles at four loci in the genome. In this study, the VNTR analysis was further validated by assessing the stability of these repeats after multiplication of the pathogen upon host-to-host transmission using a 'Ca. L. asiaticus' strain from Japan. The results showed that some tandem repeats showed detectable changes after insect transmission. To our knowledge, this is the first report to demonstrate that the repeat numbers VNTR 002 and 077 of 'Ca. L. asiaticus' change through psyllid transmission. VNTRs in the recipient plant were apparently unrelated to the growing phase of the vector. In contrast, changes in the number of tandem repeats increased with longer acquisition and inoculation access periods, whereas changes were not observed through psyllid transmission after relatively short acquisition and inoculation access periods, up to 20 and 19 days, respectively.

  18. Changes in Variable Number of Tandem Repeats in ‘Candidatus Liberibacter asiaticus’ through Insect Transmission

    PubMed Central

    2015-01-01

    Citrus greening (huanglongbing) is the most destructive citrus disease worldwide. The disease is associated with three species of ‘Candidatus Liberibacter’ among which ‘Ca. Liberibacter asiaticus’ has the widest distribution. ‘Ca. L. asiaticus’ is commonly transmitted by a phloem-feeding insect vector, the Asian citrus psyllid Diaphorina citri. A previous study showed that isolates of ‘Ca. L. asiaticus’ were clearly differentiated by variable number of tandem repeat (VNTR) profiles at four loci in the genome. In this study, the VNTR analysis was further validated by assessing the stability of these repeats after multiplication of the pathogen upon host-to-host transmission using a ‘Ca. L. asiaticus’ strain from Japan. The results showed that some tandem repeats showed detectable changes after insect transmission. To our knowledge, this is the first report to demonstrate that the repeat numbers VNTR 002 and 077 of ‘Ca. L. asiaticus’ change through psyllid transmission. VNTRs in the recipient plant were apparently unrelated to the growing phase of the vector. In contrast, changes in the number of tandem repeats increased with longer acquisition and inoculation access periods, whereas changes were not observed through psyllid transmission after relatively short acquisition and inoculation access periods, up to 20 and 19 days, respectively. PMID:26402645

  19. In vitro evaluation of the TandemHeart pediatric centrifugal pump.

    PubMed

    Svitek, Robert G; Smith, Douglas E; Magovern, James A

    2007-01-01

    The pediatric TandemHeart pump is being developed for short-term circulatory support of patients varying in size from 2 to 40 kg. The pump withdraws blood from the left atrium via cannula inserted percutaneously, either through the right internal jugular vein or transhepatically, and pumps the blood back into the arterial system via the carotid or femoral artery. High resolution stereolithography (SLA) was used to create an upper housing and impeller design, which were assembled into a functional pump prototype. Pressure-flow characteristics of the pump were determined in a blood analogue solution and compared with the pressure-flow requirements of the intended cannulation. At 5,500 rpm, the pump was able to generate 0.4 L/min of flow with a pressure rise of 325 mm Hg and 2.0 L/min with a pressure rise of 250 mm Hg. The hydraulic performance of the pump will enable at least 50% of cardiac output when the arterial cannula is placed in the carotid artery. The hemolysis of the TandemHeart pediatric pump at 5,500 rpm was compared with the BP-50 pediatric centrifugal pump in vitro using bovine blood flowing at 0.4 L/min against 250 mm Hg. The TandemHeart pump produced a similar increase in plasma free hemoglobin levels during the duration of the 6 hour test.

  20. Effects of intermediate plasmonic structures on the performance of ultra-thin-film tandem solar cells

    NASA Astrophysics Data System (ADS)

    Mashooq, Kishwar; Talukder, Muhammad Anisuzzaman

    2017-02-01

    Although solar cells can meet the increasing demand for energy of modern world, their usage is not as widespread as expected because of their high production cost and low efficiency. Thin-film and ultra-thin-film solar cells with single and multiple active layers are being investigated to reduce cost. Additionally, multiple active layers of different energy bandgaps are used in tandem in order to absorb the solar spectra more efficiently. However, the efficiency of ultra-thin-film tandem solar cells may suffer significantly mainly because of low photon absorption and current mismatch between active layers. In this work, we study the effects of intermediate plasmonic structures on the performance of ultra-thin-film tandem solar cells. We consider three structures| each with a top amorphous silicon layer and a bottom micro-crystalline silicon layer, and an intermediate plasmonic layer between them. The intermediate layer is either a metal layer with periodic holes or periodic metal strips or periodic metal nano-clusters. Using a finite difference time domain technique for incident AM 1.5 solar spectra, we show that these intermediate layers help to excite different plasmonic and photonic modes for different light polarizations, and thereby, increase the absorption of light significantly. We find that the short-circuit current density increases by 12%, 6%, and 9% when the intermediate plasmonic structure is a metal hole-array, strips, and nano-clusters, respectively, from that of a structure that does not have the intermediate plasmonic layer.

  1. Perovskite/germanium tandem: A potential high efficiency thin film solar cell design

    NASA Astrophysics Data System (ADS)

    Zi, Wei; Ren, Xiaodong; Ren, Xianpei; Wei, Qinbo; Gao, Fei; Liu, Shengzhong Frank

    2016-12-01

    Perovskite absorbs from ultraviolet (UV) to ∼800 nm, and germanium covers to 1800 nm, the combination shows excellent match in terms of solar spectrum-splitting. The optical properties of CH3NH3PbI3-xClx perovskite and single-crystalline germanium (c-Ge) tandem solar cell on a special designed substrate with triangular grating are analyzed and discussed. The finite difference time domain (FDTD) approach is used to solve the Maxwell's equations in three dimensions rigorously. By optimizing the absorption layer thickness, the current match between the top and the bottom component cells is achieved using very thin films as thin as 1500 nm. By controlling the thickness of perovskite and c-Ge to 750 nm each, high short circuit current density (Jsc) of the tandem solar cell is achieved to as high as 23.70 mA/cm2. The perovskite/c-Ge tandem thin film cell design is capable of a potential efficiency 24.88% based on the simulation.

  2. Inverted Polymeric Photovoltaic Cells and Parallel Tandems with Transparent Single Wall Carbon Nanotubes Interlayer

    NASA Astrophysics Data System (ADS)

    Mielczarek, Kamil; Cook, Alex; Zakhidov, Anvar; Kaskela, Antti; Nasibulin, Albert; Kauppinen, Esko

    2011-03-01

    We demonstrate an organic photovoltaic (OPV) monolithic multi junction cell in a parallel electrical configuration utilizing polymers with complementary absorption spectra and transparent single wall CNT (SWCNT) as an interlayer electrode (IE). Parallel tandem cells are of importance because they can append to the limited spectral coverage of available polymers and because there is no need balance current as is the case with in-series configurations. Devices comprise of polymeric sub cells where one is inverted using ZnO nanoparticles and a Mo O3 buffer layers, this inverted structure allows for the SWCNT IE to function as a cathode. Each sub cell is characterized independently and the short circuit current of the tandem device is shown to increase. Overall increase in efficiency is observed and attributed to enhanced spectral coverage by spectrally complimentary polymers and the effective use of parallel tandem architecture. We also demonstrate a semi transparent inverted OPV structure with a SWCNT electrode and a efficiency of over 3%. Supported by AFRL/Rice and Welch AT 16-17 grants.

  3. Possible Role of Natural Selection in the Formation of Tandem-Repetitive Noncoding DNA

    PubMed Central

    Stephan, W.; Cho, S.

    1994-01-01

    A simulation model of sequence-dependent amplification, unequal crossing over and mutation is analyzed. This model predicts the spontaneous formation of tandem-repetitive patterns of noncoding DNA from arbitrary sequences for a wide range of parameter values. Natural selection is found to play an essential role in this self-organizing process. Natural selection which is modeled as a mechanism for controlling the length of a nucleotide string but not the sequence itself favors the formation of tandem-repetitive structures. Two measures of sequence heterogeneity, inter-repeat variability and repeat length, are analyzed in detail. For fixed mutation rate, both inter-repeat variability and repeat length are found to increase with decreasing rates of (unequal) crossing over. The results are compared with data on micro-, mini- and satellite DNAs. The properties of minisatellites and satellite DNAs resemble the simulated structures very closely. This suggests that unequal crossing over is a dominant long-range ordering force which keeps these arrays homogeneous even in regions of very low recombination rates, such as at satellite DNA loci. Our analysis also indicates that in regions of low rates of (unequal) crossing over, inter-repeat variability is maintained at a low level at the expense of much larger repeat units (multimeric repeats), which are characteristic of satellite DNA. In contrast, the microsatellite data do not fit the proposed model well, suggesting that unequal crossing over does not act on these very short tandem arrays. PMID:8138169

  4. Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements.

    PubMed Central

    Armour, J A; Wong, Z; Wilson, V; Royle, N J; Jeffreys, A J

    1989-01-01

    We present DNA sequences flanking cloned hypervariable human minisatellites. In addition to providing confirmatory evidence that minisatellites cluster with other tandem repeats, these flanking sequences contain a high frequency of interspersed repetitive elements. These elements include a retroviral LTR-like sequence, from which one of the minisatellites appears to have expanded, and a recently described short interspersed repeat. We present our own findings concerning this element, in particular that those examples studied do not show significant evolutionary conservation, despite suggestions that the element may have a cis-acting function. Images PMID:2762114

  5. Coupled operation of the Oak Ridge isochronous cyclotron and the 25 MV tandem

    SciTech Connect

    Lord, R.S.; Ball, J.B.; Beckers, R.M.; Cleary, T.P.; Hudson, E.D.; Ludemann, C.A.; Martin, J.A.; Milner, W.T.; Mosko, S.W.; Ziegler, N.F.

    1981-01-01

    Coupled operation of the 25 MV tandem and the Oak Ridge Isochronous Cyclotron (ORIC) was achieved on January 27, 1981. A beam of 38 MeV /sup 16/O/sup 2 +/ was injected into ORIC, stripped to 8/sup +/ and accelerated to 324 MeV. Shortly afterwards, the energy was increased to the maximum design value of 25 MeV/amu (400 MeV). A spectrum taken of the scattering of this beam from a thin /sup 208/Pb target in the broad range spectrograh exhibited a resolution of 115 keV (FWHM). Performance of the system was in close agreement with that predicted from calculations.

  6. An n-CdSe/SnO/sub 2//n-Si tandem electrochemical solar cell

    SciTech Connect

    Gobrecht, J.; Nottenburg, R.; Potter, R.; Wagner, S.

    1983-11-01

    The authors demonstrate a new type of monolithic tandem junction solar cell. The cell is made up of a bottom (low energy gap) Schottky barrier and a top (high energy gap) semiconductor-electrolyte junction. By using silicon as the low gap and cadmium selenide as the high gap semiconductor we chose a pair of semiconductors which produces equal photocurrents when stacked on top of each other. They observed open-circuit voltages up to 1.21V which demonstrate addition of the output voltage of the two cells. Short-circuit currents are low, reflecting the poor quality of the CdSe film.

  7. Progress in the tandem mirror program

    SciTech Connect

    Fowler, T.K.; Borchers, R.R.

    1981-09-13

    Experimental results in TMX have confirmed the basic principles of the tandem-mirror concept. A center-cell particle confinement parameter eta tau approx. 10/sup 11/ cm/sup -3/ s has been obtained at ion temperatures around 100 eV, which is a hundred-fold improvement over single mirrors at the same temperatures. For TMX these results have been obtained at peak beta values in the center cell in the range 10 to 40%, not yet limited by MHD activity; and ion-cyclotron resonant heating (ICRH) in the Phaedrus tandem-mirror experiment has produced beta values approx. 25%, which is several times the ideal MHD limit for that device. In addition, it has been demonstrated that the end fan chambers of TMX simultaneously isolate the hot electrons from the end walls, provide adequate pumping and conveniently dispose of the exhaust plasma energy either by thermal deposition on the end wall or by direct conversion to electricity (at 48% efficiency in agreement with calculations). Also, evidence was obtained for inherent divertor action in TMX, presumably in part responsible for the observed low impurity level (<0.5% low-Z ions in the center cell).

  8. Exhaustive whole-genome tandem repeats search.

    PubMed

    Krishnan, Arun; Tang, Francis

    2004-11-01

    Approximate tandem repeats (ATR) occur frequently in the genomes of organisms, and are a source of polymorphisms observed in individuals, and thus are of interest to those studying genetic disorders. Though extensive work has been done in order to identify ATRs, there are inherent limitations with the current approaches in terms of the number of pattern sizes that can be searched or the size of the input length. This paper describes (1) a new algorithm which exhaustively finds all variable-length ATRs in a genomic sequence and (2) a precise description of, and an algorithm to significantly reduce, redundancy in the output. Our ATR definition is parameterized by a mismatch ratio p which allows for more mismatches in longer tandem repeats (and fewer in shorter). Furthermore, our algorithm is embarrassingly parallel and thus can attain near-linear speed-up on Beowulf clusters. We present results of our algorithm applied to sequences of widely differing lengths (from genes to chromosomes). Source and binaries are available on request.

  9. Identification and Validation of Evolutionarily Conserved Unusually Short Pre-mRNA Introns in the Human Genome

    PubMed Central

    Shimada, Makoto K.; Sasaki-Haraguchi, Noriko; Mayeda, Akila

    2015-01-01

    According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. Here, we provide for the first time a list of bona fide human ultra-short introns, which have never been characterized elsewhere. By conducting BLAST searches of the databases, we screened 22 introns (37–65 nt) with conserved lengths and sequences among closely related species. We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism. PMID:25961948

  10. Form-Focused Interaction in Online Tandem Learning

    ERIC Educational Resources Information Center

    O'Rourke, Breffni

    2005-01-01

    Tandem language learning--a configuration involving pairs of learners with complementary target/native languages--is an underexploited but potentially very powerful use of computer-mediated communication (CMC) in second-language pedagogy. Tandem offers the benefits of authentic, culturally grounded interaction, while also promoting a pedagogical…

  11. Monitoring Bilingualism: Pedagogical Implications of the Bilingual Tandem Analyser

    ERIC Educational Resources Information Center

    Schwienhorst, Klaus; Borgia, Alexandre

    2006-01-01

    Tandem learning is the collaborative learning partnership of two language learners with complementary language combinations, for example an Irish student learning German and a German student learning English. One of the major principles in tandem learning, apart from reciprocity and learner autonomy, is balanced bilingualism. While learners may…

  12. Monitoring Bilingualism: Pedagogical Implications of the Bilingual Tandem Analyser

    ERIC Educational Resources Information Center

    Schwienhorst, Klaus; Borgia, Alexandre

    2006-01-01

    Tandem learning is the collaborative learning partnership of two language learners with complementary language combinations, for example an Irish student learning German and a German student learning English. One of the major principles in tandem learning, apart from reciprocity and learner autonomy, is balanced bilingualism. While learners may…

  13. Summary of the tandem energy focusing explosive warhead technologies

    SciTech Connect

    Zhou, T.S.

    1996-09-26

    In this paper, on the basis of a great amount of the analysis of the tandem energy focusing explosive warhead in our country and other countries, we summarize the design demand of the tandem warhead, the delayed ignition controlling technique between the explosives, the isolating explosion protection technique and the detonator technique.

  14. A tandem-based compact dual-energy gamma generator

    SciTech Connect

    Persaud, A.; Kwan, J.W.; Leitner, M.; Leung, K.N.; Ludewigt, B.; Tanaka, N.; Waldron, W.; Wilde, S.; Antolak, A.J.; Morse, D.H.; Raber, T.

    2009-11-11

    A dual-energy tandem-type gamma generator has been developed at E.O. Lawrence Berkeley National Laboratory and Sandia National Laboratories. The tandem accelerator geometry allows higher energy nuclear reactions to be reached, thereby allowing more flexible generation of MeV-energy gammas for active interrogation applications.

  15. Negotiating Multiple Identities through eTandem Learning Experiences

    ERIC Educational Resources Information Center

    Yang, Se Jeong; Yi, Youngjoo

    2017-01-01

    Much of eTandem research has investigated either linguistic or cross-cultural aspects of second language (L2) learning, but relatively little is known about issues of identity construction in an eTandem context. Situating the study within theories and research of language learner identity, we examined ways in which two adult L2 learners (a Korean…

  16. Tandem-type pulse tube refrigerator without reservoir

    NASA Astrophysics Data System (ADS)

    Ki, Taekyung; Jeong, Sangkwon; Ko, Junseok; Park, Jiho

    2015-12-01

    In this paper, a tandem-type pulse tube refrigerator without a reservoir is discussed and investigated. For its practical application a tandem-type compressor is designed to generate two pulsating pressure waves with opposite phases, simultaneously. A tandem-type pulse tube refrigerator consists of a tandem-type compressor and two identical pulse tube refrigerators. The two identical pulse tube refrigerators share the same heat exchangers and one can be connected with the other by an inertance tube without a reservoir. In this proposed configuration, the mechanical vibration and temperature oscillations in the cold-end heat exchanger can be internally suppressed due to its intrinsic opposite-characteristic operation. To examine the quantitative evaluation of the tandem feature which does not require a reservoir in the pulse tube, an evolutionary approach has been attempted. A general structure of a pulse tube refrigerator is modified into tandem Stirling-type and GM-type machines and the transformed configuration has been simulated for tandem operation. The simulation results clearly demonstrate that a properly designed tandem-type pulse tube refrigerator without a reservoir can function favorably.

  17. Chained and tandem fixed-interval schedules of punishment1

    PubMed Central

    Silverman, Philip J.

    1971-01-01

    Pigeons' key pecks were both punished with electric shock on four-component chained and tandem fixed-interval schedules and reinforced on a variable-interval schedule of food presentation. Pecking was suppressed less in the early components of the chained schedule than in the early components of the tandem schedule. Related multiple and mixed schedules of punishment were also presented; these schedules were identical to the chained and tandem schedules, respectively, except that components changed independently of responding. Similar effects were obtained, in that responding was suppressed in all components of the mixed schedule and only in the fourth component of the multiple schedule of punishment. The performances maintained on the chained and tandem schedules of punishment were generally symmetrical to those found in analogous chained and tandem schedules of food reinforcement. PMID:16811527

  18. The physiological effects of cycling on tandem and single bicycles

    PubMed Central

    Seifert, J; Bacharach, D; Burke, E; Langenfeld, M; Snyder, A

    2003-01-01

    Objective: The purpose of this field study was to compare the physiological responses from cycling on a tandem road bicycle to those from cycling on a single road bicycle. Methods: Nine pairs of experienced, recreational tandem cyclists rode a tandem or their single bicycle for 5 min at each velocity of 19.3, 22.5, 25.8, and 29.0 kph on a flat, paved surface. Heart rate (HR), rating of perceived exertion (RPE), and lactic acid (LA) data were collected after each interval. Results: Riding a tandem resulted in lower HR, RPE, and LA mean values across the four velocities compared to the single bicycle. Mean (SD) HR, RPE, and LA for tandem and single bicycles were 126 (20.7) v 142 (20.1) bpm, 10.1 (1.7) v 11.3 (2.6), and 1.46 (1.0) mM/L v 2.36 (1.7) mM/L, respectively. No position differences were observed between the captain and stoker (front and rear positions) when both were on the tandem. Stokers had significantly lower HR, LA, and RPE values when they rode a tandem compared to a single bicycle. No statistical differences were observed between bicycles for the captains. When on the single bicycle, captains exhibited significantly lower HR, RPE, and LA values than stokers. Conclusion: Cycling on a tandem resulted in lower physiological stress than when cycling at the same velocity on a single bicycle. Cyclists were able to ride from 4.8–8.0 kph faster on a tandem than on a single bicycle at similar physiological stress. Apparently, stokers can add to power output on a tandem without adding significantly to wind resistance. PMID:12547743

  19. Electronic Tandem Language Learning (eTandem): A Third Approach to Second Language Learning for the 21st Century

    ERIC Educational Resources Information Center

    Cziko, Gary A.

    2004-01-01

    Tandem language learning occurs when two learners of different native languages work together to help each other learn the other language. First used in face-to-face contexts, Tandem is now increasingly being used by language-learning partners located in different countries who are linked via various forms of electronic communication, a context…

  20. Axisymmetric Tandem Mirrors: Stabilization and Confinement Studies

    SciTech Connect

    Post, R F; Fowler, T K; Bulmer, R; Byers, J; Hua, D; Tung, L

    2004-07-15

    The 'Kinetic Stabilizer' has been proposed as a means of MHD stabilizing an axisymmetric tandem mirror system. The K-S concept is based on theoretical studies by Ryutov, confirmed experimentally in the Gas Dynamic Trap experiment in Novosibirsk. In the K-S beams of ions are directed into the end of an 'expander' region outside the outer mirror of a tandem mirror. These ions, slowed, stagnated, and reflected as they move up the magnetic gradient, produce a low-density stabilizing plasma. At the Lawrence Livermore National Laboratory we have been conducting theoretical and computational studies of the K-S Tandem Mirror. These studies have employed a low-beta code written especially to analyze the beam injection/stabilization process, and a new code SYMTRAN (by Hua and Fowler) that solves the coupled radial and axial particle and energy transport in a K-S TM. Also, a 'legacy' MHD stability code, FLORA, has been upgraded and employed to benchmark the injection/stabilization code and to extend its results to high beta values. The FLORA code studies so far have confirmed the effectiveness of the K-S in stabilizing high-beta (40%) plasmas with stabilizer plasmas the peak pressures of which are several orders of magnitude smaller than those of the confined plasma. Also the SYMTRAN code has shown D-T plasma ignition from alpha particle energy deposition in T-M regimes with strong end plugging. Our studies have confirmed the viability of the K-S-T-M concept with respect to MHD stability and radial and axial confinement. We are continuing these studies in order to optimize the parameters and to examine means for the stabilization of possible residual instability modes, such as drift modes and 'trapped-particle' modes. These modes may in principle be controlled by tailoring the stabilizer plasma distribution and/or the radial potential distribution. In the paper the results to date of our studies are summarized and projected to scope out possible fusion-power versions of the K

  1. High efficiency InGaP solar cells for InGaP/GaAs tandem cell application

    SciTech Connect

    Takamoto, T.; Ikeda, E.; Kurita, H.; Ohmori, M.

    1994-12-31

    In this paper, high conversion efficiency single junction InGaP solar cells with n-p-p{sup +} structure are presented and their application to InGaP/GaAs monolithic tandem cells is discussed. In the InGaP cells, a best conversion efficiency of 18.48% was achieved by introducing the p{sup +} peak back surface field (BSF) layer with a high carrier concentration of 2 {times} 10{sup 18} cm{sup {minus}3}, which improved both short circuit current (Isc) and open circuit voltage (Voc). However, in the case of InGaP/GaAs tandem cells, a decrease in carrier concentration of the InGaP BSF layer, which was caused by the diffusion of Zn, was found to reduce the Isc and Voc of the tandem cell. The reduction in the carrier concentration was suppressed by using a thicker BSF layer of 0.5 {micro}m, which reduced the current density in the GaAs bottom cell. An InGaP/GaAs tandem cell with 27.3% efficiency and a high Voc of 2.418 V was obtained.

  2. T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm.

    PubMed

    Jorda, Julien; Kajava, Andrey V

    2009-10-15

    Over the last years a number of evidences have been accumulated about high incidence of tandem repeats in proteins carrying fundamental biological functions and being related to a number of human diseases. At the same time, frequently, protein repeats are strongly degenerated during evolution and, therefore, cannot be easily identified. To solve this problem, several computer programs which were based on different algorithms have been developed. Nevertheless, our tests showed that there is still room for improvement of methods for accurate and rapid detection of tandem repeats in proteins. We developed a new program called T-REKS for ab initio identification of the tandem repeats. It is based on clustering of lengths between identical short strings by using a K-means algorithm. Benchmark of the existing programs and T-REKS on several sequence datasets is presented. Our program being linked to the Protein Repeat DataBase opens the way for large-scale analysis of protein tandem repeats. T-REKS can also be applied to the nucleotide sequences. The algorithm has been implemented in JAVA, the program is available upon request at http://bioinfo.montp.cnrs.fr/?r=t-reks. Protein Repeat DataBase generated by using T-REKS is accessible at http://bioinfo.montp.cnrs.fr/?r=repeatDB.

  3. Negative deuterium ions for tandem mirror next step and tandem mirror reactors

    SciTech Connect

    Hamilton, G.W.

    1980-09-25

    Recent designs for mirror fusion reactors with good power balance include ambipolar potential plugs to reduce end losses and thermal barriers to maintain a difference in electron temperature between the large-volume central cell plasma and the confining end plugs. These designs led to several new requirements for D/sup 0/ neutral beams derived from negative ions at energies of 150 to 200 keV and possibly higher. Such beams are required for injection of fat ions into the plugs and the barrier and for charge-exchange pumping of thermal ions diffusing into the barrier. Negative ions are preferred for these purposes because of their relatively high efficiency of neutralization and their high purity of single-energy D/sup -/. Examples of injector designs for Tandem Mirror Next Step (TMNS) and Tandem Mirror Reactors (TMR) are presented.

  4. TMX-U (Tandem Mirror Experiment-Upgrade) tandem-mirror thermal-barrier experiments

    SciTech Connect

    Simonen, T.C.; Allen, S.L.; Baldwin, D.E.; Barter, J.D.; Berzins, L.V.; Carter, M.R.; Casper, T.A.; Clauser, J.F.; Coensgen, F.H.; Correll, D.L.

    1986-10-29

    Thermal-barrier experiments have been carried out in the Tandem Mirror Experiment-Upgrade (TMX-U). Measurements of nonambipolar and ambipolar radial transport show that these transport processes, as well as end losses, can be controlled at modest densities and durations. Central-cell heating methods using ion-cyclotron heating (ICH) and neutral-beam injection have been demonstrated. Potential mesurements with recently developed methods indicate that deep thermal barriers can be established.

  5. Electrospray and tandem mass spectrometry in biochemistry.

    PubMed Central

    Griffiths, W J; Jonsson, A P; Liu, S; Rai, D K; Wang, Y

    2001-01-01

    Over the last 20 years, biological MS has changed out of all recognition. This is primarily due to the development in the 1980s of 'soft ionization' methods that permit the ionization and vaporization of large, polar, and thermally labile biomolecules. These developments in ionization mode have driven the design and manufacture of smaller and cheaper mass analysers, making the mass spectrometer a routine instrument in the biochemistry laboratory today. In the present review the revolutionary 'soft ionization' methods will be discussed with particular reference to electrospray. The mass analysis of ions will be described, and the concept of tandem MS introduced. Where appropriate, examples of the application of MS in biochemistry will be provided. Although the present review will concentrate on the MS of peptides/proteins and lipids, all classes of biomolecules can be analysed, and much excellent work has been done in the fields of carbohydrate and nucleic acid biochemistry. PMID:11311115

  6. Electrospray and tandem mass spectrometry in biochemistry.

    PubMed

    Griffiths, W J; Jonsson, A P; Liu, S; Rai, D K; Wang, Y

    2001-05-01

    Over the last 20 years, biological MS has changed out of all recognition. This is primarily due to the development in the 1980s of 'soft ionization' methods that permit the ionization and vaporization of large, polar, and thermally labile biomolecules. These developments in ionization mode have driven the design and manufacture of smaller and cheaper mass analysers, making the mass spectrometer a routine instrument in the biochemistry laboratory today. In the present review the revolutionary 'soft ionization' methods will be discussed with particular reference to electrospray. The mass analysis of ions will be described, and the concept of tandem MS introduced. Where appropriate, examples of the application of MS in biochemistry will be provided. Although the present review will concentrate on the MS of peptides/proteins and lipids, all classes of biomolecules can be analysed, and much excellent work has been done in the fields of carbohydrate and nucleic acid biochemistry.

  7. Parametric systems analysis for tandem mirror hybrids

    SciTech Connect

    Lee, J.D.; Chapin, D.L.; Chi, J.W.H.

    1980-09-01

    Fusion fission systems, consisting of fissile producing fusion hybrids combining a tandem mirror fusion driver with various blanket types and net fissile consuming LWR's, have been modeled and analyzed parametrically. Analysis to date indicates that hybrids can be competitive with mined uranium when U/sub 3/O/sub 8/ cost is about 100 $/lb., adding less than 25% to present day cost of power from LWR's. Of the three blanket types considered, uranium fast fission (UFF), thorium fast fission (ThFF), and thorium fission supressed (ThFS), the ThFS blanket has a modest economic advantage under most conditions but has higher support ratios and potential safety advantages under all conditions.

  8. Protein Sequencing with Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Ziady, Assem G.; Kinter, Michael

    The recent introduction of electrospray ionization techniques that are suitable for peptides and whole proteins has allowed for the design of mass spectrometric protocols that provide accurate sequence information for proteins. The advantages gained by these approaches over traditional Edman Degradation sequencing include faster analysis and femtomole, sometimes attomole, sensitivity. The ability to efficiently identify proteins has allowed investigators to conduct studies on their differential expression or modification in response to various treatments or disease states. In this chapter, we discuss the use of electrospray tandem mass spectrometry, a technique whereby protein-derived peptides are subjected to fragmentation in the gas phase, revealing sequence information for the protein. This powerful technique has been instrumental for the study of proteins and markers associated with various disorders, including heart disease, cancer, and cystic fibrosis. We use the study of protein expression in cystic fibrosis as an example.

  9. Flute instability in the tandem mirror with the divertor/dipole regions

    SciTech Connect

    Katanuma, I.; Masaki, S.; Sato, S.; Sekiya, K.; Ichimura, M.; Imai, T.

    2011-11-15

    The numerical simulation is performed in GAMMA10 A-divertor magnetic configuration, which is a candidate of remodeled device of the GAMMA10 tandem mirror [M. Inutake et al., Phys. Rev. Lett. 55, 939 (1985)]. Both divertor and dipole regions are included in the numerical calculation, which is a new point. The electron short circuit effect along x-point, therefore, is not assumed so that it is not used the boundary condition of the electrostatic perturbations being zero at the separatrix on which the magnetic field lines pass through x-point. The simulation results reveal that the dipole field plays a role of a good magnetic field line curvature to the GAMMA10 A-divertor, and so the flute modes are stabilized without help of electron short circuit effects.

  10. A tandem-based compact dual-energy gamma generator.

    PubMed

    Persaud, A; Kwan, J W; Leitner, M; Leung, K-N; Ludewigt, B; Tanaka, N; Waldron, W; Wilde, S; Antolak, A J; Morse, D H; Raber, T

    2010-02-01

    A dual-energy tandem-type gamma generator has been developed at E. O. Lawrence Berkeley National Laboratory and Sandia National Laboratories. The tandem accelerator geometry allows higher energy nuclear reactions to be reached, thereby allowing more flexible generation of MeV-energy gammas for active interrogation applications. Both positively charged ions and atoms of hydrogen are created from negative ions via a gas stripper. In this paper, we show first results of the working tandem-based gamma generator and that a gas stripper can be utilized in a compact source design. Preliminary results of monoenergetic gamma production are shown.

  11. Classroom Tandem--Outlining a Model for Language Learning and Instruction

    ERIC Educational Resources Information Center

    Karjalainen, Katri; Pörn, Michaela; Rusk, Fredrik; Björkskog, Linda

    2013-01-01

    The aim of this paper is to outline classroom tandem by comparing it with informal tandem learning contexts and other language instruction methods. Classroom tandem is used for second language instruction in mixed language groups in the subjects of Finnish and Swedish as L2. Tandem learning entails that two persons with different mother tongues…

  12. 47 CFR 36.124 - Tandem switching equipment-Category 2.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 2 2011-10-01 2011-10-01 false Tandem switching equipment-Category 2. 36.124... Central Office Equipment § 36.124 Tandem switching equipment—Category 2. (a) Tandem switching equipment is contained in Accounts 2210, 2211, and 2212. It includes all switching equipment in a tandem central office...

  13. Use of ultrasonic and pepsin treatment in tandem for collagen extraction from meat industry by-products.

    PubMed

    Ran, Xue-Guang; Wang, Ling-Yun

    2014-02-01

    Relatively little attention is paid to collagen-rich cattle short tendons (musculus extensor communis, musculus flexor digitorum, musculus digitorum profundis) as a source of high content and relatively pure collagen, a meat-processing by-product that is used to a minimal extent. Thus, suitable extraction processes from a meat production by-product to gain intact collagen is promising, which thus become interesting from an economic and environmental point of view. Two extraction methods were compared: a 48 h pepsin treatment using 0.5 mol L⁻¹ acetic acid and an extraction using pepsin treatment after ultrasonic treatment in a 0.5 mol L⁻¹ acetic acid solution (the total ultrasonic and pepsin treatment time was 48 h). The results indicated that the optimal conditions for the extraction of collagen from cattle tendon with the ultrasonic-pepsin tandem method is: 4°C, tendon pre-swollen for 12 h in 0.5 mol L⁻¹ acetic acid, pepsin amount: 50 U mg⁻¹ of sample, ultrasonic-pepsin tandem treatment time for 18 h and 30 h, respectively. Extracted cattle tendon collagen using ultrasonic and pepsin treatment in tandem was characterised by amino acid analysis, SDS-PAGE, FT-IR, solubility and thermal denaturation temperature. The results show that the ultrasonic-pepsin tandem method can effectively improve the efficiency of pepsin extraction of natural collagen without any compromise of the resultant collagen quality. This study provides a favourable process to deal with poorly extractable residue by use of ultrasonic and pepsin treatment in tandem. Extracted collagen possesses an intact molecular structure, which is useful and particularly important for its biomedical applications, such as drug delivery systems, wound dressings, and scaffolds. © 2013 Society of Chemical Industry.

  14. Maine Caucasian population DNA database using twelve short tandem repeat loci.

    PubMed

    Kupferschmid, T D; Calicchio, T; Budowle, B

    1999-03-01

    A population study of Caucasians residing in Maine was conducted using the AmpF1STR Profiler PCR Amplification Kit and the AmpF1STR Profiler Plus PCR Amplification Kit (Applied Biosystems Division (ABD) of Perkin Elmer, Foster City, CA). The kits contain the reagents necessary to amplify 12 different STR loci and the gender marker Amelogenin using two multiplex PCR, each containing nine STR loci. Thus, there is an overlap of six STR loci. The 12 STR loci are TH01, TPOX, CSF1PO, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820. These loci represent 12 of the 13 core loci selected by the CODIS STR standardization project. Dye-labeled amplification products were separated and detected using the capillary electrophoresis instrument ABI Prism 310 Genetic Analyzer. Allele frequencies were determined for the 12 STR loci. Statistical analysis of the data included Hardy-Weinburg equilibrium (HWE) analysis, pairwise independence testing, power of discrimination (PD), and probability of exclusion (PE).

  15. Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)

    PubMed Central

    Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

    2014-01-01

    Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community. PMID:25148383

  16. [Analysis of genetics and genomics of short tandem repeat loci commonly used in Kinship Testing].

    PubMed

    Li, Cheng-Tao; Guo, Hong; Zhao, Zhen-Min; Li, Li

    2008-06-01

    Since the foundation of FBI laboratory's Combined DNA Index System (CODIS) a decade ago, the 13 CODIS STR loci of the system as well as the recently developed Penta D, Penta E, D2S1338 and D19S433 loci have been widely used by kinship testing laboratories worldwide and have played an important role in the field of Kinship Testing and in construction of criminal database. This article systemically analyzed the characteristics of STR loci information and its genomic information analyzed through search of a variety of database including Webof Knowledge, Elsevier and Internet resources. The up-to-date application of the commonly used STR loci in recent years is also reviewed.

  17. Short Gel, Long Gradient Liquid Chromatography Tandem Mass Spectrometry to Discover Urinary Biomarkers of Chronic Pancreatitis

    PubMed Central

    Paulo, Joao A.; Kadiyala, Vivek; Brizard, Scott; Banks, Peter A.; Conwell, Darwin L.; Steen, Hanno

    2014-01-01

    Background Chronic pancreatitis (CP) is currently diagnosed using invasive endoscopic as well as radiation and non-radiation-based imaging techniques. However, urine can be safely and non-invasively collected and as such may offer a superior alternative to current techniques of CP diagnosis. We use mass spectrometry-based methods to discover proteins which are exclusive to or differentially abundant in urine of chronic pancreatitis patients. Methods We have performed a comparative quantitative proteomic analysis of urine collected from 5 healthy controls and 5 severe CP patients. Proteins from urine were fractionated briefly on SDS-PAGE and subsequently digested in-gel with trypsin. The resulting peptides were fractionated for 3 hours by reversed-phase liquid chromatography in-line with a mass spectrometer. ProteinPilot software and the QSPEC algorithm identified proteins and determined statistically significant differences between cohorts. In addition, we used a third cohort of non-CP disease patients to filter out those proteins which may be indicative of an ailment other than CP. Results We identified over 600 proteins from urine, of which several hundred were either exclusive to or differ quantitatively between healthy controls and severe CP patients. Members of the cathepsin protein family were of significantly higher abundance in the severe CP cohort. In addition, we have identified a core set of 50 proteins in all 15 samples, 25 of which showed no significant difference among the cohorts. Conclusions Proteomic analysis identified differentially abundant proteins in healthy controls and severe CP patients. Such proteins represent an initial set of targets for directed proteomics experiments for further validation studies. However, larger cohorts will be required to determine if these differences have statistically significant diagnostic potential. PMID:25346780

  18. Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis).

    PubMed

    Biswas, Manosh Kumar; Xu, Qiang; Mayer, Christoph; Deng, Xiuxin

    2014-01-01

    Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.

  19. Potential of 13 linked autosomal short tandem repeat loci in pairwise kinship analysis.

    PubMed

    Liu, Qiu-Ling; Xue, Li; Wu, Wei-Wei; He, Xin; Liu, Kai-Yan; Zhao, Hu; Lu, De-Jian

    2016-10-01

    In this study, a panel of 13 STR loci locate on chromosome 3, 4, and 17 (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2404, D4S2364, AC001348A, AC001348B, D17S975, and D17S1294) were assessed for pairwise kinship analysis. Map distances between these STR loci ranged from 0.07 cM to 97.03 cM. The population genetic study of Chinese Han population showed that linkage disequilibrium exists in two clusters of closely linked markers (D4S2404-D4S2364 and D17S975-D17S1294), in which the recombination fractions were 0.0026 and 0.0001, respectively. The recombination fractions derived from the Rutgers Map for the closely linked markers (genetic distance < 0.5 cM) were significant underestimates in comparison to those of direct observation of STR transmissions in families. When effect of linkage on pairwise kinship testing was evaluated by comparing likelihood ratio (LR) values taking linkage into account, overall LR values increased. But extremely low LRs were also observed. Finally, the power of the 13 STR loci to discriminate relationship among full-sibs, half-sibs, grandparent-grandchild, uncle-niece, and unrelated pairs was assessed with a category fraction. The results showed that about 72.64% of full-sib pairs and about 82.84% of unrelated pairs could be classified correctly. But the category fractions of second-degree relationships drastically reduced to 7.34-35.48%. If only pairs of grandparent-grandchild, half-sibs, and uncle-niece were distinguished, the category fraction was 0.5512, 0.1147, and 0.4362, respectively. Our study results demonstrated that linked STRs were helpful to differentiate the most frequent relationships in pairwise kinship analysis.

  20. Analysis of Rapidly Mutating Y Chromosome Short Tandem Repeats (RM Y-STRs).

    PubMed

    Hadi, Sibte

    2016-01-01

    Rapidly mutating (RM) Y-STRs were recently identified and can help to differentiate between paternally related males in paternity and forensic casework. Normal Y-STRs are often used in casework due to their paternal inheritance, which can help to resolve kinship cases, and identify male components in male/female mixtures; however, more discriminating profiles are obtained if rapidly mutating Y-STRs are used. Previously two or three multiplex PCRs have been used to amplify 13 RM Y-STRs; here, an assay amplifying these 13 markers in a single multiplex PCR is described. Commercially available male control DNA samples have been genotyped during the validation of this assay, thus providing a tool for calibrating genotyping results. It is expected that the assay will provide a niche tool for genotyping casework samples.

  1. Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog.

    PubMed

    Salim, D C; Akimoto, A A; Carvalho, C B; Oliveira, S F; Grisolia, C K; Moreira, J R; Klautau-Guimarães, M N

    2007-06-20

    The maned wolf (Chrysocyon brachyurus) is the largest South American canid. Habitat loss and fragmentation, due to agricultural expansion and predatory hunting, are the main threats to this species. It is included in the official list of threatened wildlife species in Brazil, and is also protected by IUCN and CITES. Highly variable genetic markers such as microsatellites have the potential to resolve genetic relationships at all levels of the population structure (among individuals, demes or metapopulations) and also to identify the evolutionary unit for strategies for the conservation of the species. Tests were carried out to verify whether a class of highly polymorphic tetranucleotide repeats described for the domestic dog effectively amplifies DNA in the maned wolf. All five loci studied were amplified; however, one of these, was shown to be monomorphic in 69 maned wolf samples. The average allele number and estimated heterozygosity per polymorphic locus were 4.3 and 67%, respectively. The genetic variability found for this species, which is considered threatened with extinction, showed similar results when compared to studies of other canids.

  2. Analysis of forensically used autosomal short tandem repeat markers in Polish and neighboring populations.

    PubMed

    Soltyszewski, Ireneusz; Plocienniczak, Andrzej; Fabricius, Hans Ake; Kornienko, Igor; Vodolazhsky, Dmitrij; Parson, Walther; Hradil, Roman; Schmitter, Hermann; Ivanov, Pavel; Kuzniar, Piotr; Malyarchuk, Boris A; Grzybowski, Tomasz; Woźniak, Marcin; Henke, Jurgen; Henke, Lotte; Olkhovets, Sergiv; Voitenko, Vladimir; Lagus, Vita; Ficek, Andrej; Minárik, Gabriel; de Knijff, Peter; Rebała, Krzysztof; Wysocka, Joanna; Kapińska, Ewa; Cybulska, Lidia; Mikulich, Alexei I; Tsybovsky, Iosif S; Szczerkowska, Zofia; Krajewski, Paweł; Ploski, Rafał

    2008-06-01

    The purpose of this study was to evaluate the homogeneity of Polish populations with respect to STRs chosen as core markers of the Polish Forensic National DNA Intelligence Database, and to provide reference allele frequencies and to explore the genetic interrelationship between Poland and neighboring countries. The allele frequency distribution of 10 STRs included in the SGMplus kit was analyzed among 2176 unrelated individuals from 6 regional Polish populations and among 4321 individuals from Germany (three samples), Austria, The Netherlands, Sweden, Czech Republic, Slovakia, Belarus, Ukraine and the Russian Federation (six samples). The statistical approach consisted of AMOVA, calculation of pairwise Rst values and analysis by multidimensional scaling. We found homogeneity of present day Poland and consistent differences between Polish and German populations which contrasted with relative similarities between Russian and German populations. These discrepancies between genetic and geographic distances were confirmed by analysis of an independent data set on Y chromosome STRs. Migrations of Goths, Viking influences, German settlements in the region of Volga river and/or forced population resettlements and other events related to World War II are the historic events which might have caused these finding.

  3. Variation at 4 short tandem repeat loci in 8 population groups of India.

    PubMed

    Mukherjee, N; Majumder, P P; Roy, B; Roy, M; Dey, B; Chakraborty, M; Banerjee, S

    1999-06-01

    We have determined the nature and extent of variation at 4 STR loci (CSF1P0, TPOX, TH01, VWA) in 8 caste and tribal population groups of eastern and northern India. Large differences in allele frequencies among the groups were found. Average heterozygosities in all populations were high (approximately 80%). The overall extent of gene differentiation among the 8 groups was high (GST = 0.04). The nature of genomic affinities based on these 4 STR loci does not completely agree with our earlier finding based on classical genetic markers that geographic proximity of habitat has a greater influence on genetic similarity between populations than sociocultural proximity does.

  4. Population variation at the CODIS core short tandem repeat loci in Europeans.

    PubMed

    Budowle, B; Chakraborty, R

    2001-03-01

    Substantial STR population data exist to estimate F(ST) (or theta) values across Europeans. Eleven populations across Europe were analyzed, and the estimate over all 13 CODIS core STR loci is 0.0028. This value is much less than the conservative estimate of 0.01 advocated by the second National Research Council Report in 1996. Because of the low value for theta, whether independence is assumed or an adjustment for substructure is employed, there is little practical consequence for forensic purposes for estimating the frequency of a multiple locus DNA profile. If theta is used, a value of 0.01 is very conservative for Europeans. The same STR population data can be used for evolutionary studies on Europeans, and the calculated genetic distances are consistent with the ethnohistory of the populations.

  5. Light management of tandem solar cells on nanostructured substrates

    NASA Astrophysics Data System (ADS)

    Chin, Alan H.; Keshavarz, Majid; Wang, Guo; Yu, Rosaline; Niu, Xinwei; Yang, Liyou

    2017-04-01

    We report the use of nanostructured substrates as a simple approach to improve the performance of tandem micromorph silicon solar cells. In the proposed approach, nanostructured substrates are produced using a low-cost, self-assembled growth process. The use of a nanostructured substrate coated with a thick transparent conductive oxide electrode layer enables the conformal deposition of the tandem solar cell absorber layers while allowing the solar cell to exhibit a modified surface morphology caused by the underlying nanostructured morphology. Using this nanostructured substrate approach, we demonstrated a 78% relative enhancement in the conversion efficiency of a tandem micromorph silicon cell on a nanostructured substrate compared to a standard tandem micromorph cell deposited onto a flat substrate.

  6. SYMTRAN - A Time-dependent Symmetric Tandem Mirror Transport Code

    SciTech Connect

    Hua, D; Fowler, T

    2004-06-15

    A time-dependent version of the steady-state radial transport model in symmetric tandem mirrors in Ref. [1] has been coded up and first tests performed. Our code, named SYMTRAN, is an adaptation of the earlier SPHERE code for spheromaks, now modified for tandem mirror physics. Motivated by Post's new concept of kinetic stabilization of symmetric mirrors, it is an extension of the earlier TAMRAC rate-equation code omitting radial transport [2], which successfully accounted for experimental results in TMX. The SYMTRAN code differs from the earlier tandem mirror radial transport code TMT in that our code is focused on axisymmetric tandem mirrors and classical diffusion, whereas TMT emphasized non-ambipolar transport in TMX and MFTF-B due to yin-yang plugs and non-symmetric transitions between the plugs and axisymmetric center cell. Both codes exhibit interesting but different non-linear behavior.

  7. Detailed balance limit of the efficiency of tandem solar cells

    NASA Astrophysics Data System (ADS)

    de Vos, A.

    1980-05-01

    The fundamental (detailed balance) limit of the performance of a tandem structure is presented. The model takes into account the fact that a particular cell is not only illuminated by part of the solar irradiance but also by the electroluminescence of other cells of the set. Whereas under 1 sun irradiance a single solar cell only converts 30% of the solar energy, a tandem structure of two cells can convert 42%, a tandem structure of three cells can convert 49%, etc. Under the highest possible light concentration, these efficiencies are 40% (one cell), 55% (two cells), 63% (three cells), etc. The model also allows one to predict the ideal efficiency of a stack with an infinite number of solar cells. Such a tandem system can convert 68% of the unconcentrated sunlight, and 86% of the concentrated sunlight.

  8. D STAND DELIVERY END OF #44 TANDEM BREAKDOWN MILL WITH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    D STAND DELIVERY END OF #44 TANDEM BREAKDOWN MILL WITH UPCOILER. BACKUP ROLLS, 40 TONS. WORK ROLLS, 20 TONS., C. 1900. OPERATING SPEED, 600'/MINUTE. AUTOMATIC GAUGE CONTROL. - American Brass Foundry, 70 Sayre Street, Buffalo, Erie County, NY

  9. Design of tandem mirror reactors with thermal barriers

    SciTech Connect

    Carlson, G.A.

    1980-01-01

    End-plug technologies for tandem mirror reactors include high-field superconducting magnets, neutral beam injectors, and gyrotrons for electron cyclotron resonant heating (ECRH). In addition to their normal use for sustenance of the end-plug plasmas, neutral beam injectors are used for ''pumping'' trapped ions from the thermal barrier regions by charge exchange. An extra function of the axially directed pump beams is the removal of thermalized alpha particles from the reactor. The principles of tandem mirror operation with thermal barriers will be demonstrated in the upgrade of the Tandem Mirror Experiment (TMX-U) in 1981 and the tandem configuration of the Mirror fusion Test Facility (MFTF-B) in 1984.

  10. Plasma-wall interactions in tandem mirror machines

    SciTech Connect

    Allen, S.L.

    1984-11-01

    A description is presented of the plasma-surface interactions in thermal-barrier tandem-mirror machines. The thermal-barrier mode of axial confinement is an integral part of a tandem mirror, and it dictates the required plasma conditions, particularly at the surface of the plasma. For this reason, a qualitative discussion of the thermal barrier is presented first in Section 2. A brief description of the experimental configuration used in tandem mirrors to create the thermal barrier is then examined in detail in Section 3; the TMX-U and MFTF-B machines are used as specific examples. In Section 4, the relevant plasma-surface interaction issues are addressed, and experimental results from currently operating tandom mirror machines are included. Section 5 is both a summary and a discussion of future work concerned with plasma-surface interactions in tandem mirrors.

  11. Monolithic Perovskite Silicon Tandem Solar Cells with Advanced Optics

    SciTech Connect

    Goldschmidt, Jan C.; Bett, Alexander J.; Bivour, Martin; Blasi, Benedikt; Eisenlohr, Johannes; Kohlstadt, Markus; Lee, Seunghun; Mastroianni, Simone; Mundt, Laura; Mundus, Markus; Ndione, Paul; Reichel, Christian; Schubert, Martin; Schulze, Patricia S.; Tucher, Nico; Veit, Clemens; Veurman, Welmoed; Wienands, Karl; Winkler, Kristina; Wurfel, Uli; Glunz, Stefan W.; Hermle, Martin

    2016-11-14

    For high efficiency monolithic perovskite silicon tandem solar cells, we develop low-temperature processes for the perovskite top cell, rear-side light trapping, optimized perovskite growth, transparent contacts and adapted characterization methods.

  12. Tandem wheel drop-legs for standard truck trailer

    NASA Technical Reports Server (NTRS)

    Cantwell, W.; Selstad, R.

    1970-01-01

    Tandem wheel drop-leg device provides a semitrailer with fore and aft mobility that allows it to be moved without a prime mover. The modified drop-legs have trunnion dual wheels and an adjustable brace.

  13. 5. GENERAL VIEW OF UNITEDTOD TWIN TANDEM STEAM ENGINE. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. GENERAL VIEW OF UNITED-TOD TWIN TANDEM STEAM ENGINE. - Republic Iron & Steel Company, Youngstown Works, Blooming Mill & Blooming Mill Engines, North of Poland Avenue, Youngstown, Mahoning County, OH

  14. Tandem Solar Cells from Solution-Processed CdTe and PbS Quantum Dots Using a ZnTe-ZnO Tunnel Junction.

    PubMed

    Crisp, Ryan W; Pach, Gregory F; Kurley, J Matthew; France, Ryan M; Reese, Matthew O; Nanayakkara, Sanjini U; MacLeod, Bradley A; Talapin, Dmitri V; Beard, Matthew C; Luther, Joseph M

    2017-02-08

    We developed a monolithic CdTe-PbS tandem solar cell architecture in which both the CdTe and PbS absorber layers are solution-processed from nanocrystal inks. Due to their tunable nature, PbS quantum dots (QDs), with a controllable band gap between 0.4 and ∼1.6 eV, are a promising candidate for a bottom absorber layer in tandem photovoltaics. In the detailed balance limit, the ideal configuration of a CdTe (Eg = 1.5 eV)-PbS tandem structure assumes infinite thickness of the absorber layers and requires the PbS band gap to be 0.75 eV to theoretically achieve a power conversion efficiency (PCE) of 45%. However, modeling shows that by allowing the thickness of the CdTe layer to vary, a tandem with efficiency over 40% is achievable using bottom cell band gaps ranging from 0.68 and 1.16 eV. In a first step toward developing this technology, we explore CdTe-PbS tandem devices by developing a ZnTe-ZnO tunnel junction, which appropriately combines the two subcells in series. We examine the basic characteristics of the solar cells as a function of layer thickness and bottom-cell band gap and demonstrate open-circuit voltages in excess of 1.1 V with matched short circuit current density of 10 mA/cm(2) in prototype devices.

  15. Improved efficiency of perovskite-silicon tandem solar cell near the matched optical absorption between the subcells

    NASA Astrophysics Data System (ADS)

    Iftiquar, S. M.; Jung, Junhee; Yi, Junsin

    2017-10-01

    Current matching in a tandem solar cell is significant, because in a mismatched device the lowest current generating subcell becomes the current limiting component, and overall device efficiency remains lower than that could be obtained in the current matched device. Recent reports on methyl ammonium lead iodide (MAPbI3) based thin film solar cell has drawn interest to a perovskite-silicon tandem solar cell. Therefore, we investigated such a tandem solar cell theoretically. We used a MAPbI3 based top and heterojunction with intrinsic thin layer silicon (HIT) bottom subcell. Optimization of the device structure was carried out by varying thickness of perovskite layer of top-cell from 50 to 1000 nm, while thickness of active layer of the HIT cell was kept constant, to 500 µm. Single-junction solar cell, formed with the bottom subcell had open circuit voltage (V oc) of 705.1 mV, short circuit current density (J sc) of 28.22 mA cm‑2, fill factor (FF) of 0.82 and efficiency of 16.4% under AM1.5G insolation. A relatively low thickness (150 nm) of the perovskite absorber layer was found optimum for the top-subcell to achieve best efficiency of the tandem cell, partly because of intermediate reflection at the interface between the two cells. We obtained a maximum of 20.92% efficiency of the tandem solar cell, which is higher by a factor of 1.27 from the starting HIT cell and a factor 1.47 higher from the perovskite cell efficiency. J sc of the optimized tandem cell was 13.06 mA cm‑2. This was achieved near the matching optical absorption or current-density of the component subcells. For a practical application, the device used in our investigation was without textured front surface. An ordinary HIT bottom-cell was used with lower J sc. Therefore, with an improved HIT subcell, efficiency of the tandem cell, higher than 21% will be achievable.

  16. Engineering problems of tandem-mirror reactors

    SciTech Connect

    Moir, R.W.; Barr, W.L.; Boghosian, B.M.

    1981-10-22

    We have completed a comparative evaluation of several end plug configurations for tandem mirror fusion reactors with thermal barriers. The axi-cell configuration has been selected for further study and will be the basis for a detailed conceptual design study to be carried out over the next two years. The axi-cell end plug has a simple mirror cell produced by two circular coils followed by a transition coil and a yin-yang pair, which provides for MHD stability. This paper discusses some of the many engineering problems facing the designer. We estimated the direct cost to be 2$/W/sub e/. Assuming total (direct and indirect) costs to be twice this number, we need to reduce total costs by factors between 1.7 and 2.3 to compete with future LWRs levelized cost of electricity. These reductions may be possible by designing magnets producing over 20T made possible by use of combinations of superconducting and normal conducting coils as well as improvements in performance and cost of neutral beam and microwave power systems. Scientific and technological understanding and innovation are needed in the area of thermal barrier pumping - a process by which unwanted particles are removed (pumped) from certain regions of velocity and real space in the end plug. Removal of exhaust fuel ions, fusion ash and impurities by action of a halo plasma and plasma dump in the mirror end region is another challenging engineering problem discussed in this paper.

  17. Light Signaling Mechanism of Two Tandem Bacteriophytochromes

    PubMed Central

    Yang, Xiaojing; Stojković, Emina A.; Ozarowski, Wesley B.; Kuk, Jane; Davydova, Erna; Moffat, Keith

    2015-01-01

    RpBphP2 and RpBphP3, two tandem bacteriophytochromes from the photosynthetic bacterium R. palustris, share high sequence identity but exhibit distinct photoconversion behavior. Unlike the canonical RpBphP2, RpBphP3 photoconverts to an unusual nearred-absorbing (Pnr) state; both are required for synthesis of light harvesting complexes under low-light conditions. Here we report the crystal structures of the photosensory core modules of RpBphP2 and RpBphP3. Despite different quaternary structures, RpBphP2 and RpBphP3 adopt nearly identical tertiary structures. The RpBphP3 structure reveals “tongue-and-groove” interactions at the interface between the GAF and PHY domains. A single mutation in the PRxSF motif at the GAF-PHY interface abolishes light-induced formation of the Pnr state in RpBphP3, possibly due to altered structural rigidity of the chromophore-binding pocket. Structural comparisons suggest that long-range signaling involves structural rearrangement of the helical spine at the dimer interface. These structures together with mutational studies provide insights into photoconversion and long-range signaling mechanism in phytochromes. PMID:26095026

  18. Software dependability in the Tandem GUARDIAN system

    NASA Technical Reports Server (NTRS)

    Lee, Inhwan; Iyer, Ravishankar K.

    1995-01-01

    Based on extensive field failure data for Tandem's GUARDIAN operating system this paper discusses evaluation of the dependability of operational software. Software faults considered are major defects that result in processor failures and invoke backup processes to take over. The paper categorizes the underlying causes of software failures and evaluates the effectiveness of the process pair technique in tolerating software faults. A model to describe the impact of software faults on the reliability of an overall system is proposed. The model is used to evaluate the significance of key factors that determine software dependability and to identify areas for improvement. An analysis of the data shows that about 77% of processor failures that are initially considered due to software are confirmed as software problems. The analysis shows that the use of process pairs to provide checkpointing and restart (originally intended for tolerating hardware faults) allows the system to tolerate about 75% of reported software faults that result in processor failures. The loose coupling between processors, which results in the backup execution (the processor state and the sequence of events) being different from the original execution, is a major reason for the measured software fault tolerance. Over two-thirds (72%) of measured software failures are recurrences of previously reported faults. Modeling, based on the data, shows that, in addition to reducing the number of software faults, software dependability can be enhanced by reducing the recurrence rate.

  19. Tandem-mirror technology demonstration facility

    SciTech Connect

    Fowler, T.K.; Logan, B.G.

    1981-09-18

    Preliminary calculations at LLNL indicate that a Technology Demonstration Facility (TDF) consisting of a tandem mirror machine about the size of TMX could begin providing fusion nuclear engineering data as early as 1988. With high density operation based on physics already demonstrated in TMX, this machine would produce 12 MW of DT neutrons in steady-state from a plasma column 0.08 m in radius and 8 m in length. Allowing space for neutral beam injectors at each end of the column, this would permit testing of blanket modules and components at 1 MW/m/sup 2/ neutron wall load over a cylindrical surface 8 m/sup 2/ in area at a radius of 0.25 m; or one could irradiate thousands of small samples at 2 MW/m/sup 2/ at r = 0.125 m (4 m/sup 2/ area). With improved end-plug physics to be tested in TMX-Upgrade in 1982-83, the wall load at 0.25 m could be increased to 2 MW/m/sup 2/ (4 MW/m/sup 2/ at r = 0.125 m). Construction of the TDF could begin in FY84 and be completed in 4 to 5 years, at a cost roughly estimated as $700M in '81 dollars including engineering and 30% contingency.

  20. Transcription of tandemly repetitive DNA: functional roles.

    PubMed

    Biscotti, Maria Assunta; Canapa, Adriana; Forconi, Mariko; Olmo, Ettore; Barucca, Marco

    2015-09-01

    A considerable fraction of the eukaryotic genome is made up of satellite DNA constituted of tandemly repeated sequences. These elements are mainly located at centromeres, pericentromeres, and telomeres and are major components of constitutive heterochromatin. Although originally satellite DNA was thought silent and inert, an increasing number of studies are providing evidence on its transcriptional activity supporting, on the contrary, an unexpected dynamicity. This review summarizes the multiple structural roles of satellite noncoding RNAs at chromosome level. Indeed, satellite noncoding RNAs play a role in the establishment of a heterochromatic state at centromere and telomere. These highly condensed structures are indispensable to preserve chromosome integrity and genome stability, preventing recombination events, and ensuring the correct chromosome pairing and segregation. Moreover, these RNA molecules seem to be involved also in maintaining centromere identity and in elongation, capping, and replication of telomere. Finally, the abnormal variation of centromeric and pericentromeric DNA transcription across major eukaryotic lineages in stress condition and disease has evidenced the critical role that these transcripts may play and the potentially dire consequences for the organism.

  1. X!!Tandem, an Improved Method for Running X!Tandem in Parallel on Collections of Commodity Computers

    PubMed Central

    Bjornson, Robert D.; Carriero, Nicholas J.; Colangelo, Christopher; Shifman, Mark; Cheung, Kei-Hoi; Miller, Perry L.; Williams, Kenneth

    2013-01-01

    The widespread use of mass spectrometry for protein identification has created a demand for computationally efficient methods of matching mass spectrometry data to protein databases. A search using X!Tandem, a popular and representative program, can require hours or days to complete, particularly when missed cleavages and post-translational modifications are considered. Existing techniques for accelerating X!Tandem by employing parallelism are unsatisfactory for a variety of reasons. The paper describes a parallelization of X!Tandem, called X!!Tandem, that shows excellent speedups on commodity hardware and produces the same results as the original program. Furthermore, the parallelization technique used is unusual and potentially useful for parallelizing other complex programs. PMID:17902638

  2. Structural Correlation of the Neck Coil with the Coiled-coil (CC1)-Forkhead-associated (FHA) Tandem for Active Kinesin-3 KIF13A.

    PubMed

    Ren, Jinqi; Huo, Lin; Wang, Wenjuan; Zhang, Yong; Li, Wei; Lou, Jizhong; Xu, Tao; Feng, Wei

    2016-02-12

    Processive kinesin motors often contain a coiled-coil neck that controls the directionality and processivity. However, the neck coil (NC) of kinesin-3 is too short to form a stable coiled-coil dimer. Here, we found that the coiled-coil (CC1)-forkhead-associated (FHA) tandem (that is connected to NC by Pro-390) of kinesin-3 KIF13A assembles as an extended dimer. With the removal of Pro-390, the NC-CC1 tandem of KIF13A unexpectedly forms a continuous coiled-coil dimer that can be well aligned into the CC1-FHA dimer. The reverse introduction of Pro-390 breaks the NC-CC1 coiled-coil dimer but provides the intrinsic flexibility to couple NC with the CC1-FHA tandem. Mutations of either NC, CC1, or the FHA domain all significantly impaired the motor activity. Thus, the three elements within the NC-CC1-FHA tandem of KIF13A are structurally interrelated to form a stable dimer for activating the motor. This work also provides the first direct structural evidence to support the formation of a coiled-coil neck by the short characteristic neck domain of kinesin-3.

  3. Structural Correlation of the Neck Coil with the Coiled-coil (CC1)-Forkhead-associated (FHA) Tandem for Active Kinesin-3 KIF13A*

    PubMed Central

    Ren, Jinqi; Huo, Lin; Wang, Wenjuan; Zhang, Yong; Li, Wei; Lou, Jizhong; Xu, Tao; Feng, Wei

    2016-01-01

    Processive kinesin motors often contain a coiled-coil neck that controls the directionality and processivity. However, the neck coil (NC) of kinesin-3 is too short to form a stable coiled-coil dimer. Here, we found that the coiled-coil (CC1)-forkhead-associated (FHA) tandem (that is connected to NC by Pro-390) of kinesin-3 KIF13A assembles as an extended dimer. With the removal of Pro-390, the NC-CC1 tandem of KIF13A unexpectedly forms a continuous coiled-coil dimer that can be well aligned into the CC1-FHA dimer. The reverse introduction of Pro-390 breaks the NC-CC1 coiled-coil dimer but provides the intrinsic flexibility to couple NC with the CC1-FHA tandem. Mutations of either NC, CC1, or the FHA domain all significantly impaired the motor activity. Thus, the three elements within the NC-CC1-FHA tandem of KIF13A are structurally interrelated to form a stable dimer for activating the motor. This work also provides the first direct structural evidence to support the formation of a coiled-coil neck by the short characteristic neck domain of kinesin-3. PMID:26680000

  4. Altered Methylation in Tandem Repeat Element and Elemental Component Levels in Inhalable Air Particles

    PubMed Central

    Hou, Lifang; Zhang, Xiao; Zheng, Yinan; Wang, Sheng; Dou, Chang; Guo, Liqiong; Byun, Hyang-Min; Motta, Valeria; McCracken, John; Díaz, Anaité; Kang, Choong-Min; Koutrakis, Petros; Bertazzi, Pier Alberto; Li, Jingyun; Schwartz, Joel; Baccarelli, Andrea A.

    2014-01-01

    Exposure to particulate matter (PM) has been associated with lung cancer risk in epidemiology investigations. Elemental components of PM have been suggested to have critical roles in PM toxicity, but the molecular mechanisms underlying their association with cancer risks remain poorly understood. DNA methylation has emerged as a promising biomarker for environmental-related diseases, including lung cancer. In this study, we evaluated the effects of PM elemental components on methylation of three tandem repeats in a highly-exposed population in Beijing, China. The Beijing Truck Driver Air Pollution Study was conducted shortly before the 2008 Beijing Olympic Games (June 15-July 27, 2008) and included 60 truck drivers and 60 office workers. On two days separated by 1-2 weeks, we measured blood DNA methylation of SATα, NBL2, D4Z4, and personal exposure to eight elemental components in PM2.5, including aluminum (Al), silicon (Si), sulfur (S), potassium (K), calcium (Ca) titanium (Ti), iron (Fe), and zinc (Zn). We estimated the associations of individual elemental component with each tandem repeat methylation in generalized estimating equations (GEE) models adjusted for PM2.5 mass and other covariates. Out of the eight examined elements, NBL2 methylation was positively associated with concentrations of Si (0.121, 95%CI: 0.030; 0.212, FDR=0.047) and Ca (0.065, 95%CI: 0.014; 0.115, FDR=0.047) in truck drivers. In office workers, SATα methylation was positively associated with concentrations of S (0.115, 95%CI: 0.034; 0.196, FDR=0.042). PM-associated differences in blood tandem-repeat methylation may help detect biological effects of the exposure and identify individuals who may eventually experience higher lung cancer risk. PMID:24273195

  5. A Tandem Cycling Program: Feasibility and Physical Performance Outcomes in People With Parkinson Disease.

    PubMed

    McGough, Ellen L; Robinson, Cynthia A; Nelson, Mark D; Houle, Raymond; Fraser, Gabriell; Handley, Leslie; Jones, Emilie R; Amtmann, Dagmar; Kelly, Valerie E

    2016-10-01

    Individuals with Parkinson disease (PD) have motor and nonmotor impairments that interfere with exercise participation. The purpose of this study was to examine the feasibility and physical performance outcomes of a community-based indoor tandem cycling program that was designed to facilitate a higher cadence, consistency, and intensity of training. Forty-one participants with mild to moderate PD were enrolled. A high-cadence cycling protocol using mechanically augmented (or forced) exercise on a tandem bicycle was adapted for our program. Participants cycled 3 times per week for 10 weeks. Feasibility measures included program retention, attendance, and adverse events, as well as the ability to reach training goals for heart rate (HR) and cadence. Physical performance outcomes included the Berg Balance Scale (BBS), Short Physical Performance Battery (SPPB), Five-Times-Sit-to-Stand (FTSTS) Test, Timed Up and Go (TUG), and gait parameters during usual and fast-paced walking. Program feasibility was demonstrated with a high attendance rate (96%) and retention rate (100%). There were no adverse events. The majority of participants reached their exercise training goals for target HR (87%) and cadence (95%). Statistically significant physical performance improvement (P < 0.05) was observed across domains of gait, balance, and mobility, suggesting a slowing or reversal of functional decline as a result of this cycling program. Program feasibility and improved physical performance outcomes were demonstrated in individuals with mild to moderate PD participating in a community-based indoor tandem cycling program.Video Abstract available for more insights from the authors (see supplemental digital content 1, http://links.lww.com/JNPT/A146).

  6. Dominant short repeated sequences in bacterial genomes.

    PubMed

    Avershina, Ekaterina; Rudi, Knut

    2015-03-01

    We use a novel multidimensional searching approach to present the first exhaustive search for all possible repeated sequences in 166 genomes selected to cover the bacterial domain. We found an overrepresentation of repeated sequences in all but one of the genomes. The most prevalent repeats by far were related to interspaced short palindromic repeats (CRISPRs)—conferring bacterial adaptive immunity. We identified a deep branching clade of thermophilic Firmicutes containing the highest number of CRISPR repeats. We also identified a high prevalence of tandem repeated heptamers. In addition, we identified GC-rich repeats that could potentially be involved in recombination events. Finally, we identified repeats in a 16322 amino acid mega protein (involved in biofilm formation) and inverted repeats flanking miniature transposable elements (MITEs). In conclusion, the exhaustive search for repeated sequences identified new elements and distribution of these, which has implications for understanding both the ecology and evolution of bacteria.

  7. Measurements of Short-Lived Fission Isomers

    NASA Astrophysics Data System (ADS)

    Finch, Sean; Bhike, Megha; Howell, Calvin; Krishichayan, Fnu; Tornow, Werner

    2016-09-01

    Fission yields of the short lived isomers 134mTe (T1 / 2 = 162 ns) and 136mXe (T1 / 2 = 2 . 95 μs) were measured for 235U and 238U. The isomers were detected by the γ rays associated with the decay of the isomeric states using high-purity germanium detectors. Fission was induced using both monoenergetic γ rays and neutrons. At TUNL's High-Intensity Gamma-ray Source (HI γS), γ rays of 9 and 11 MeV were produced . Monoenergetic 8 MeV neutrons were produced at TUNL's tandem accelerator laboratory. Both beams were pulsed to allow for precise time-gated spectroscopy of both prompt and delayed γ rays following fission. This technique offers a non-destructive probe of special nuclear materials that is sensitive to the isotopic identity of the fissile material.

  8. Short bowel syndrome

    MedlinePlus

    Small intestine insufficiency; Short gut syndrome; Necrotizing enterocolitis - short bowel ... The small intestine absorbs much of the nutrients found in foods we eat. When one half or more of our small ...

  9. Shortness-of-Breath

    MedlinePlus

    ... can lead to shortness of breath include anxiety, panic attacks, anemia and even constipation. The experience of shortness ... are used to treat patients with anxiety or panic attacks. Other commonly used drugs include bronchodilators to widen ...

  10. Shortness of Breath

    MedlinePlus

    ... Wheezing Worsening of pre-existing shortness of breath Self-care To help keep chronic shortness of breath ... JA, et al. Dyspnea. In: Rosen's Emergency Medicine: Concepts and Clinical Practice. 8th ed. Philadelphia, Pa.: Saunders ...

  11. Minimizing Shortness of Breath

    MedlinePlus

    ... and begin to limit our daily activities. Increase Awareness Occupational therapists find that shortness of breath is ... first steps for patients is to increase their awareness and help them recognize symptoms of shortness of ...

  12. Improving organic tandem solar cells based on water-processed nanoparticles by quantitative 3D nanoimaging.

    PubMed

    Pedersen, E B L; Angmo, D; Dam, H F; Thydén, K T S; Andersen, T R; Skjønsfjell, E T B; Krebs, F C; Holler, M; Diaz, A; Guizar-Sicairos, M; Breiby, D W; Andreasen, J W

    2015-08-28

    Organic solar cells have great potential for upscaling due to roll-to-roll processing and a low energy payback time, making them an attractive sustainable energy source for the future. Active layers coated with water-dispersible Landfester particles enable greater control of the layer formation and easier access to the printing industry, which has reduced the use of organic solvents since the 1980s. Through ptychographic X-ray computed tomography (PXCT), we image quantitatively a roll-to-roll coated photovoltaic tandem stack consisting of one bulk heterojunction active layer and one Landfester particle active layer. We extract the layered morphology with structural and density information including the porosity present in the various layers and the silver electrode with high resolution in 3D. The Landfester particle layer is found to have an undesired morphology with negatively correlated top- and bottom interfaces, wide thickness distribution and only partial surface coverage causing electric short circuits through the layer. By top coating a polymer material onto the Landfester nanoparticles we eliminate the structural defects of the layer such as porosity and roughness, and achieve the increased performance larger than 1 V expected for a tandem cell. This study highlights that quantitative imaging of weakly scattering stacked layers of organic materials has become feasible by PXCT, and that this information cannot be obtained by other methods. In the present study, this technique specifically reveals the need to improve the coatability and layer formation of Landfester nanoparticles, thus allowing improved solar cells to be produced.

  13. Quantitative acylcarnitine determination by UHPLC-MS/MS--Going beyond tandem MS acylcarnitine "profiles".

    PubMed

    Minkler, Paul E; Stoll, Maria S K; Ingalls, Stephen T; Kerner, Janos; Hoppel, Charles L

    2015-12-01

    Tandem MS "profiling" of acylcarnitines and amino acids was conceived as a first-tier screening method, and its application to expanded newborn screening has been enormously successful. However, unlike amino acid screening (which uses amino acid analysis as its second-tier validation of screening results), acylcarnitine "profiling" also assumed the role of second-tier validation, due to the lack of a generally accepted second-tier acylcarnitine determination method. In this report, we present results from the application of our validated UHPLC-MS/MS second-tier method for the quantification of total carnitine, free carnitine, butyrobetaine, and acylcarnitines to patient samples with known diagnoses: malonic acidemia, short-chain acyl-CoA dehydrogenase deficiency (SCADD) or isobutyryl-CoA dehydrogenase deficiency (IBD), 3-methyl-crotonyl carboxylase deficiency (3-MCC) or ß-ketothiolase deficiency (BKT), and methylmalonic acidemia (MMA). We demonstrate the assay's ability to separate constitutional isomers and diastereomeric acylcarnitines and generate values with a high level of accuracy and precision. These capabilities are unavailable when using tandem MS "profiles". We also show examples of research interest, where separation of acylcarnitine species and accurate and precise acylcarnitine quantification is necessary.

  14. A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats

    PubMed Central

    Curtis, Edward A; Liu, David R

    2014-01-01

    Recently, we used in vitro selection to identify a new class of naturally occurring GTP aptamer called the G motif. Here we report the discovery and characterization of a second class of naturally occurring GTP aptamer, the “CA motif.” The primary sequence of this aptamer is unusual in that it consists entirely of tandem repeats of CA-rich motifs as short as three nucleotides. Several active variants of the CA motif aptamer lack the ability to form consecutive Watson-Crick base pairs in any register, while others consist of repeats containing only cytidine and adenosine residues, indicating that noncanonical interactions play important roles in its structure. The circular dichroism spectrum of the CA motif aptamer is distinct from that of A-form RNA and other major classes of nucleic acid structures. Bioinformatic searches indicate that the CA motif is absent from most archaeal and bacterial genomes, but occurs in at least 70 percent of approximately 400 eukaryotic genomes examined. These searches also uncovered several phylogenetically conserved examples of the CA motif in rodent (mouse and rat) genomes. Together, these results reveal the existence of a second class of naturally occurring GTP aptamer whose sequence requirements, like that of the G motif, are not consistent with those of a canonical secondary structure. They also indicate a new and unexpected potential biochemical activity of certain naturally occurring tandem repeats. PMID:24824832

  15. Panchromatic quantum-dot-sensitized solar cells based on a parallel tandem structure.

    PubMed

    Zhou, Na; Yang, Yueyong; Huang, Xiaoming; Wu, Huijue; Luo, Yanhong; Li, Dongmei; Meng, Qingbo

    2013-04-01

    A tandem-structure sensitized solar cell, comprising different inorganic semiconductor quantum dots (QDs) as sensitizers in two different compartments, has been designed for the first time with the aim of extending the light-absorption range of current technologies. In this system, the CdS/CdSe co-sensitized quantum-dot solar cell (QDSC) is in the upper part, whereas the PbS/CdS co-sensitized QDSC is in the lower part; these are connected in parallel with each other. In the middle of the tandem solar cell, a Cu2 S mesh counter electrode is employed. By optimizing the electrode thickness and QD-deposition time, short-circuit photocurrent density values of as high as 25.12 mA cm(-2) have been achieved; this value is nearly equal to the sum of the two constituent QD-sensitized devices and gives rise to a solar power-conversion efficiency of 5.06 %.

  16. LPE-GaAs and LBSF-Si solar cells for tandem concentrator application

    SciTech Connect

    Blieske, U.; Sterk, S.; Bett, A.; Schumacher, J.; Wettling, W.; Marti, A.; Terron, M.J.; Luque, A.

    1994-12-31

    Design and efficiency measurements of a mechanically stacked concentrator tandem solar cell are presented. The GaA cell was grown by the LPE etch-back-regrowth method and has a diameter of 4 mm. The silicon solar cell is a high efficient LBSF concentrator solar cell of 5 mm diameter. Special care was taken to optimize the antireflection coatings on the back and front side of the GaAs solar cell. Both cells were processed at FhG-ISE in Freiburg. Their short circuit currents were measured at the ISE calibration laboratory under AM 1.5d conditions. The efficiency measurements were performed at UPM-IES in Madrid under outdoor conditions. At 27 suns (AM 1.5d, 25 C) the GaAs cell showed an efficiency of 22.9% and the silicon cell an efficiency of 2.9%. The two single cell efficiencies add to a tandem efficiency of 25.8% for the four terminal operation.

  17. High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry.

    PubMed Central

    Ducret, A.; Van Oostveen, I.; Eng, J. K.; Yates, J. R.; Aebersold, R.

    1998-01-01

    We describe an integrated workstation for the automated, high-throughput, and conclusive identification of proteins by reverse-phase chromatography electrospray ionization tandem mass spectrometry. The instrumentation consists of a refrigerated autosampler, a submicrobore reverse-phase liquid chromatograph, and an electrospray triple quadrupole mass spectrometer. For protein identification, enzymatic digests of either homogeneous polypeptides or simple protein mixtures were generated and loaded into the autosampler. Samples were sequentially injected every 32 min. Ions of eluting peptides were automatically selected by the mass spectrometer and subjected to collision-induced dissociation. Following each run, the resulting tandem mass spectra were automatically analyzed by SEQUEST, a program that correlates uninterpreted peptide fragmentation patterns with amino acid sequences contained in databases. Protein identification was established by SEQUEST_SUMMARY a program that combines the SEQUEST scores of peptides originating from the same protein and ranks the cumulative results in a short summary. The workstation's performance was demonstrated by the unattended identification of 90 proteins from the yeast Saccharomyces cerevisiae, which were separated by high-resolution two-dimensional PAGE. The system was found to be very robust and identification was reliably and conclusively established for proteins if quantities exceeding 1-5 pmol were applied to the gel. The level of automation, the throughput, and the reliability of the results suggest that this system will be useful for the many projects that require the characterization of large numbers of proteins. PMID:9541403

  18. Atomically Altered Hematite for Highly Efficient Perovskite Tandem Water Splitting Devices.

    PubMed

    Gurudayal, Gurudayal; Abraham John, Rohit; Boix, Pablo P; Yi, Chenyi; Shi, Chen; Scott, Mary C; Veldhuis, Sjoerd A; Minor, Andrew M; Zakeer, Shaik M; Wong, Lydia; Graetzel, Michael; Mathews, Nripan

    2017-04-02

    Photoelectrochemical (PEC) cells are attractive for storing solar energy in chemical bonds through cleaving of water into oxygen and hydrogen. Although hematite (a-Fe2O3) is a promising photoanode material due to its chemical stability, suitable band gap, low cost and environmental friendliness, its performance is limited by short carrier lifetimes, poor conductivity and sluggish kinetics leading to low (solar-to-hydrogen) STH efficiency. Herein, we combine solution based hydrothermal growth and a post-growth surface exposure through atomic layer deposition (ALD) to show a dramatic enhancement of the efficiency for water photolysis. These modified photoanodes show a high photocurrent of 3.12 mAcm-2 at 1.23 V vs. RHE, (> 5 times higher than Fe2O3) and a plateau photocurrent of 4.5 mAcm-2 at 1.5 V vs. RHE. We demonstrate that thesephotoanodes in tandem with a CH3NH3PbI3 perovskite solar cell achieves overall unassisted water splitting with an STH conversion efficiency of 3.4%, constituting a new benchmark for hematite based tandem systems.

  19. Parallel Tandems of Dye Sensitized Solar Cells with CNT Collector

    NASA Astrophysics Data System (ADS)

    Velten, Josef; Yuan, Chao-Chen; Zakhidov, Anvar

    2009-03-01

    In this presentation, we demonstrate the fabrication of monolithic parallel tandem dye sensitized solar cells using a semitransparent layer of carbon nanotubes. Each DSC sub-cell has titania photoelectrode with two different dyes: N 719 and N 749, which absorb light in different parts of solar spectrum. This layer of carbon nanotubes laminated on highly porous polymeric Millipore filter acts as both the collector of charge carrier and as the catalyst of the I/I3^- redox reaction that completes the function of the cell, overall allowing easier fabrication for tandem solar cell devices, with a potential for creating flexible devices in the future. The parallel tandem shows the total photocurrent which is nearly the sum of two Isc currents of constituent cells, and total Voc, which is average of two Voc, while conventional in-series DSC tandems show the lowest Voc and slightly increased Isc[1]. Thus the higher efficiency can be achieved in parallel DSC tandems, and we discuss the physical reasons for this effect. [1] Yanagida, et.al. J. of Photochemistry and Photobiology A: Chemistry Volume 164, Issues 1-3, 1 June 2004, Pages 33-39

  20. Cooperative cell motility during tandem locomotion of amoeboid cells

    PubMed Central

    Bastounis, Effie; Álvarez-González, Begoña; del Álamo, Juan C.; Lasheras, Juan C.; Firtel, Richard A.

    2016-01-01

    Streams of migratory cells are initiated by the formation of tandem pairs of cells connected head to tail to which other cells subsequently adhere. The mechanisms regulating the transition from single to streaming cell migration remain elusive, although several molecules have been suggested to be involved. In this work, we investigate the mechanics of the locomotion of Dictyostelium tandem pairs by analyzing the spatiotemporal evolution of their traction adhesions (TAs). We find that in migrating wild-type tandem pairs, each cell exerts traction forces on stationary sites (∼80% of the time), and the trailing cell reuses the location of the TAs of the leading cell. Both leading and trailing cells form contractile dipoles and synchronize the formation of new frontal TAs with ∼54-s time delay. Cells not expressing the lectin discoidin I or moving on discoidin I–coated substrata form fewer tandems, but the trailing cell still reuses the locations of the TAs of the leading cell, suggesting that discoidin I is not responsible for a possible chemically driven synchronization process. The migration dynamics of the tandems indicate that their TAs’ reuse results from the mechanical synchronization of the leading and trailing cells’ protrusions and retractions (motility cycles) aided by the cell–cell adhesions. PMID:26912787

  1. High-Efficiency Polycrystalline Thin Film Tandem Solar Cells.

    PubMed

    Kranz, Lukas; Abate, Antonio; Feurer, Thomas; Fu, Fan; Avancini, Enrico; Löckinger, Johannes; Reinhard, Patrick; Zakeeruddin, Shaik M; Grätzel, Michael; Buecheler, Stephan; Tiwari, Ayodhya N

    2015-07-16

    A promising way to enhance the efficiency of CIGS solar cells is by combining them with perovskite solar cells in tandem devices. However, so far, such tandem devices had limited efficiency due to challenges in developing NIR-transparent perovskite top cells, which allow photons with energy below the perovskite band gap to be transmitted to the bottom cell. Here, a process for the fabrication of NIR-transparent perovskite solar cells is presented, which enables power conversion efficiencies up to 12.1% combined with an average sub-band gap transmission of 71% for photons with wavelength between 800 and 1000 nm. The combination of a NIR-transparent perovskite top cell with a CIGS bottom cell enabled a tandem device with 19.5% efficiency, which is the highest reported efficiency for a polycrystalline thin film tandem solar cell. Future developments of perovskite/CIGS tandem devices are discussed and prospects for devices with efficiency toward and above 27% are given.

  2. Test of the Tandem transmission at low terminal voltages

    SciTech Connect

    Rehm, K.E.; Blumenthal, D.; Gehring, J.

    1995-08-01

    For a planned experiment with {sup 18}F beams at energies below 1 MeV/u the transmission of the Tandem-Linac system was investigated. The energies required in the experiment are typically around 600 keV/u, which for the most abundant charge states for F(4{sup +}) corresponds to terminal voltages between 2-3 MV. We studied the transmission from the source to the tandem accelerator and to the spectrograph in area II with {sup 18}O and {sup 19}F beams using two different approaches. In the first method only the tandem accelerator was used producing a 14-MeV DC {sup 18}O beam. In the second method a pulsed beam was accelerated to 33 MeV with the tandem accelerator followed by deceleration to 14 MeV with the first 9 resonators of ATLAS. The total transmission from ion source to target was in both cases about 10%. Because of the smaller complexity we used the first method for the {sup 18}F experiment. In future runs we are planning to use the electrostatic lens in the terminal of the tandem to improve the overall transmission.

  3. Design of a new tandem wings hybrid airship

    NASA Astrophysics Data System (ADS)

    Li, Feng; Ye, ZhengYin; Gao, Chao

    2012-10-01

    It is scientifically important science value and engineering promising to develop the buoyancy-lift integrated hybrid airship for high attitude platform. Through the numerical method, a new tandem wings hybrid airship with both higher utility value and economy efficiency was obtained and its total performance and technical parameters were analyzed in detail. In order to further improve the lift-drag characteristics, we implemented the optimization design for aerodynamic configuration of tandem wings hybrid airship via the response surface method. The results indicate that the tandem wings hybrid airship has considerable volume efficiency and higher aerodynamic characteristics. After optimization, the lift-drag ratio of this hybrid airship was increased by 6.08%. In a given gross lift condition, tandem wings hybrid airship may provide more payload and specific productivity. Furthermore, the size of tandem airship is smaller so the demand for skin flexible materials can be reduced. Results of this study could serve as a new approach to designing buoyancy-lifting integrated hybrid airship.

  4. The Tandem-ALPI-PIAVE accelerator complex of LNL

    SciTech Connect

    Ur, C. A.

    2013-07-18

    Heavy ion beams are delivered at the Laboratori Nazionali di Legnaro by the accelerator complex Tandem-ALPI-PIAVE. The Tandem XTU is a Van de Graaff accelerator normally operated at terminal voltages of up to about 15 MV. The Tandem accelerator can be operated in stand-alone mode or as an injector for the linac booster ALPI. The linear accelerator ALPI is built of superconducting resonant cavities and consists of a low-beta branch, particularly important for the acceleration of the heavier mass ions, a medium-beta branch, and a high-beta branch. ALPI can be operated also with the PIAVE injector that consists of a superconducting linac and an ECR source. The PIAVE source was mainly used for the acceleration of intense noble gas beams but most recently also a first metallic beam was delivered to the users. The accelerator complex delivers beams of ions from protons to gold in three experimental areas on 11 different beam lines. A rich scientific activity is ongoing at the Tandem-ALPI-PIAVE accelerator complex, beam time being shared between nuclear physics research and applied and interdisciplinary physics research. An overview of the present status and perspectives of the Tandem-ALPI-PIAVE complex and its physics program is given in the present paper.

  5. TassDB: a database of alternative tandem splice sites.

    PubMed

    Hiller, Michael; Nikolajewa, Swetlana; Huse, Klaus; Szafranski, Karol; Rosenstiel, Philip; Schuster, Stefan; Backofen, Rolf; Platzer, Matthias

    2007-01-01

    Subtle alternative splice events at tandem splice sites are frequent in eukaryotes and substantially increase the complexity of transcriptomes and proteomes. We have developed a relational database, TassDB (TAndem Splice Site DataBase), which stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. These splice events are of subtle nature since they mostly result in the insertion/deletion of a single amino acid or the substitution of one amino acid by two others. Currently, TassDB contains 114 554 tandem splice sites of eight species, 5209 of which have EST/mRNA evidence for alternative splicing. In addition, human SNPs that affect NAGNAG acceptors are annotated. The database provides a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download large datasets. This database should facilitate further experimental studies and large-scale bioinformatics analyses of tandem splice sites. The database is available at http://helios.informatik.uni-freiburg.de/TassDB/.

  6. Selection against tandem splice sites affecting structured protein regions.

    PubMed

    Hiller, Michael; Szafranski, Karol; Huse, Klaus; Backofen, Rolf; Platzer, Matthias

    2008-03-21

    Alternative selection of splice sites in tandem donors and acceptors is a major mode of alternative splicing. Here, we analyzed whether in-frame tandem sites leading to subtle mRNA insertions/deletions of 3, 6, or 9 nucleotides are under natural selection. We found multiple lines of evidence that the human protein coding sequences are under selection against such in-frame tandem splice events, indicating that these events are often deleterious. The strength of selection is not homogeneous within the coding sequence as protein regions that fold into a fixed 3D structure (intrinsically ordered) are under stronger selection, especially against sites with a strong minor splice site. Investigating structures of functional protein domains, we found that tandem acceptors are preferentially located at the domain surface and outside structural elements such as helices and sheets. Using three-species comparisons, we estimate that more than half of all mutations that create NAGNAG acceptors in the coding region have been eliminated by selection. We estimate that ~2,400 introns are under selection against possessing a tandem site.

  7. Management of light absorption in extraordinary optical transmission based ultra-thin-film tandem solar cells

    SciTech Connect

    Mashooq, Kishwar; Talukder, Muhammad Anisuzzaman

    2016-05-21

    Although ultra-thin-film solar cells can be attractive in reducing the cost, they suffer from low absorption as the thickness of the active layer is usually much smaller than the wavelength of incident light. Different nano-photonic techniques, including plasmonic structures, are being explored to increase the light absorption in ultra-thin-film solar cells. More than one layer of active materials with different energy bandgaps can be used in tandem to increase the light absorption as well. However, due to different amount of light absorption in different active layers, photo-generated currents in different active layers will not be the same. The current mismatch between the tandem layers makes them ineffective in increasing the efficiency. In this work, we investigate the light absorption properties of tandem solar cells with two ultra-thin active layers working as two subcells and a metal layer with periodically perforated holes in-between the two subcells. While the metal layer helps to overcome the current mismatch, the periodic holes increase the absorption of incident light by helping extraordinary optical transmission of the incident light from the top to the bottom subcell, and by coupling the incident light to plasmonic and photonic modes within ultra-thin active layers. We extensively study the effects of the geometry of holes in the intermediate metal layer on the light absorption properties of tandem solar cells with ultra-thin active layers. We also study how different metals in the intermediate layer affect the light absorption; how the geometry of holes in the intermediate layer affects the absorption when the active layer materials are changed; and how the intermediate metal layer affects the collection of photo-generated electron-hole pairs at the terminals. We find that in a solar cell with 6,6-phenyl C61-butyric acid methyl ester top subcell and copper indium gallium selenide bottom subcell, if the periodic holes in the metal layer are square or

  8. Management of light absorption in extraordinary optical transmission based ultra-thin-film tandem solar cells

    NASA Astrophysics Data System (ADS)

    Mashooq, Kishwar; Talukder, Muhammad Anisuzzaman

    2016-05-01

    Although ultra-thin-film solar cells can be attractive in reducing the cost, they suffer from low absorption as the thickness of the active layer is usually much smaller than the wavelength of incident light. Different nano-photonic techniques, including plasmonic structures, are being explored to increase the light absorption in ultra-thin-film solar cells. More than one layer of active materials with different energy bandgaps can be used in tandem to increase the light absorption as well. However, due to different amount of light absorption in different active layers, photo-generated currents in different active layers will not be the same. The current mismatch between the tandem layers makes them ineffective in increasing the efficiency. In this work, we investigate the light absorption properties of tandem solar cells with two ultra-thin active layers working as two subcells and a metal layer with periodically perforated holes in-between the two subcells. While the metal layer helps to overcome the current mismatch, the periodic holes increase the absorption of incident light by helping extraordinary optical transmission of the incident light from the top to the bottom subcell, and by coupling the incident light to plasmonic and photonic modes within ultra-thin active layers. We extensively study the effects of the geometry of holes in the intermediate metal layer on the light absorption properties of tandem solar cells with ultra-thin active layers. We also study how different metals in the intermediate layer affect the light absorption; how the geometry of holes in the intermediate layer affects the absorption when the active layer materials are changed; and how the intermediate metal layer affects the collection of photo-generated electron-hole pairs at the terminals. We find that in a solar cell with 6,6-phenyl C61-butyric acid methyl ester top subcell and copper indium gallium selenide bottom subcell, if the periodic holes in the metal layer are square or

  9. Multiple-Locus Variable-Number Tandem-Repeat Analysis in Genotyping Yersinia enterocolitica Strains from Human and Porcine Origins

    PubMed Central

    Laukkanen-Ninios, R.; Ortiz Martínez, P.; Siitonen, A.; Fredriksson-Ahomaa, M.; Korkeala, H.

    2013-01-01

    Sporadic and epidemiologically linked Yersinia enterocolitica strains (n = 379) isolated from fecal samples from human patients, tonsil or fecal samples from pigs collected at slaughterhouses, and pork samples collected at meat stores were genotyped using multiple-locus variable-number tandem-repeat analysis (MLVA) with six loci, i.e., V2A, V4, V5, V6, V7, and V9. In total, 312 different MLVA types were found. Similar types were detected (i) in fecal samples collected from human patients over 2 to 3 consecutive years, (ii) in samples from humans and pigs, and (iii) in samples from pigs that originated from the same farms. Among porcine strains, we found farm-specific MLVA profiles. Variations in the numbers of tandem repeats from one to four for variable-number tandem-repeat (VNTR) loci V2A, V5, V6, and V7 were observed within a farm. MLVA was applicable for serotypes O:3, O:5,27, and O:9 and appeared to be a highly discriminating tool for distinguishing sporadic and outbreak-related strains. With long-term use, interpretation of the results became more challenging due to variations in more-discriminating loci, as was observed for strains originating from pig farms. Additionally, we encountered unexpectedly short V2A VNTR fragments and sequenced them. According to the sequencing results, updated guidelines for interpreting V2A VNTR results were prepared. PMID:23637293

  10. Multiple-locus variable-number tandem-repeat analysis in genotyping Yersinia enterocolitica strains from human and porcine origins.

    PubMed

    Virtanen, S; Laukkanen-Ninios, R; Ortiz Martínez, P; Siitonen, A; Fredriksson-Ahomaa, M; Korkeala, H

    2013-07-01

    Sporadic and epidemiologically linked Yersinia enterocolitica strains (n = 379) isolated from fecal samples from human patients, tonsil or fecal samples from pigs collected at slaughterhouses, and pork samples collected at meat stores were genotyped using multiple-locus variable-number tandem-repeat analysis (MLVA) with six loci, i.e., V2A, V4, V5, V6, V7, and V9. In total, 312 different MLVA types were found. Similar types were detected (i) in fecal samples collected from human patients over 2 to 3 consecutive years, (ii) in samples from humans and pigs, and (iii) in samples from pigs that originated from the same farms. Among porcine strains, we found farm-specific MLVA profiles. Variations in the numbers of tandem repeats from one to four for variable-number tandem-repeat (VNTR) loci V2A, V5, V6, and V7 were observed within a farm. MLVA was applicable for serotypes O:3, O:5,27, and O:9 and appeared to be a highly discriminating tool for distinguishing sporadic and outbreak-related strains. With long-term use, interpretation of the results became more challenging due to variations in more-discriminating loci, as was observed for strains originating from pig farms. Additionally, we encountered unexpectedly short V2A VNTR fragments and sequenced them. According to the sequencing results, updated guidelines for interpreting V2A VNTR results were prepared.

  11. Rare disorders of metabolism with elevated butyryl- and isobutyryl-carnitine detected by tandem mass spectrometry newborn screening.

    PubMed

    Koeberl, Dwight D; Young, Sarah P; Gregersen, Niels S; Vockley, Jerry; Smith, Wendy E; Benjamin, Daniel Kelly; An, Yan; Weavil, Susan D; Chaing, Shu H; Bali, Deeksha; McDonald, Marie T; Kishnani, Priya S; Chen, Y-T; Millington, David S

    2003-08-01

    Tandem mass spectrometry was adopted for newborn screening by North Carolina in April 1999. Since then, three infants with short-chain acyl-CoA dehydrogenase (SCAD) and one with isobutyryl-CoA dehydrogenase deficiency were detected on the basis of elevated butyrylcarnitine/isobutyrylcarnitine (C4-carnitine) concentrations in newborn blood spots analyzed by tandem mass spectrometry. For three SCAD-deficient infants, biochemical evaluation included a plasma acylcarnitine profile with markedly elevated C4-carnitine, urine organic acid analysis with markedly elevated ethylmalonic and 2-methylsuccinic acids, and markedly elevated [U-13C]butyrylcarnitine concentrations in medium from fibroblasts incubated with [U-13C]palmitic acid and excess l-carnitine, consistent with classic SCAD deficiency. Two of three infants diagnosed with classic SCAD deficiency remained asymptomatic; however, the third infant presented with seizures and a cerebral infarct at 10 wk of age. All three infants had putatively inactivating mutations in both alleles of the SCAD gene. The highly elevated plasma C4-carnitine levels in the three infants detected by newborn screening tandem mass spectrometry differentiated them from infants and children who were homozygous or compound heterozygous for one of two SCAD gene susceptibility variations; for the latter group the C4-carnitine levels were normal. Isobutyryl-CoA dehydrogenase deficiency in a fourth infant was confirmed after isolated elevation of C4-carnitine in the acylcarnitine profile.

  12. The query execution engine in Tandem`s new ServerWare SQL product

    SciTech Connect

    Celis, P.; Zeller, H.

    1996-12-31

    Tandem has re-written its SQL compiler and its query execution engine into a new product that will be available on multiple operating systems. The new product uses a novel query execution engine and we will highlight the unique aspects of the new engine. ServerWare SQL uses a data flow and scheduler driven task model to execute queries. Tasks communicate either via in-memory queues or via interprocess communication. Partitioned, pipelined, or independent operations are executed in parallel. By adding new task types the model can be easily extended. Parallelism in a distributed memory environment is implemented as a special {open_quotes}Exchange{close_quotes} task type, as in the Volcano research prototype. Scheduling and load balancing are performed by separate scheduler tasks.

  13. Counter-Rotating Tandem Motor Drilling System

    SciTech Connect

    Kent Perry

    2009-04-30

    Gas Technology Institute (GTI), in partnership with Dennis Tool Company (DTC), has worked to develop an advanced drill bit system to be used with microhole drilling assemblies. One of the main objectives of this project was to utilize new and existing coiled tubing and slimhole drilling technologies to develop Microhole Technology (MHT) so as to make significant reductions in the cost of E&P down to 5000 feet in wellbores as small as 3.5 inches in diameter. This new technology was developed to work toward the DOE's goal of enabling domestic shallow oil and gas wells to be drilled inexpensively compared to wells drilled utilizing conventional drilling practices. Overall drilling costs can be lowered by drilling a well as quickly as possible. For this reason, a high drilling rate of penetration is always desired. In general, high drilling rates of penetration (ROP) can be achieved by increasing the weight on bit and increasing the rotary speed of the bit. As the weight on bit is increased, the cutting inserts penetrate deeper into the rock, resulting in a deeper depth of cut. As the depth of cut increases, the amount of torque required to turn the bit also increases. The Counter-Rotating Tandem Motor Drilling System (CRTMDS) was planned to achieve high rate of penetration (ROP) resulting in the reduction of the drilling cost. The system includes two counter-rotating cutter systems to reduce or eliminate the reactive torque the drillpipe or coiled tubing must resist. This would allow the application of maximum weight-on-bit and rotational velocities that a coiled tubing drilling unit is capable of delivering. Several variations of the CRTDMS were designed, manufactured and tested. The original tests failed leading to design modifications. Two versions of the modified system were tested and showed that the concept is both positive and practical; however, the tests showed that for the system to be robust and durable, borehole diameter should be substantially larger than

  14. Identifying tandem Ankyrin repeats in protein structures.

    PubMed

    Chakrabarty, Broto; Parekh, Nita

    2014-12-30

    Tandem repetition of structural motifs in proteins is frequently observed across all forms of life. Topology of repeating unit and its frequency of occurrence are associated to a wide range of structural and functional roles in diverse proteins, and defects in repeat proteins have been associated with a number of diseases. It is thus desirable to accurately identify specific repeat type and its copy number. Weak evolutionary constraints on repeat units and insertions/deletions between them make their identification difficult at the sequence level and structure based approaches are desired. The proposed graph spectral approach is based on protein structure represented as a graph for detecting one of the most frequently observed structural repeats, Ankyrin repeat. It has been shown in a large number of studies that 3-dimensional topology of a protein structure is well captured by a graph, making it possible to analyze a complex protein structure as a mathematical entity. In this study we show that eigen spectra profile of a protein structure graph exhibits a unique repetitive profile for contiguous repeating units enabling the detection of the repeat region and the repeat type. The proposed approach uses a non-redundant set of 58 Ankyrin proteins to define rules for the detection of Ankyrin repeat motifs. It is evaluated on a set of 370 proteins comprising 125 known Ankyrin proteins and remaining non-solenoid proteins and the prediction compared with UniProt annotation, sequence-based approach, RADAR, and structure-based approach, ConSole. To show the efficacy of the approach, we analyzed the complete PDB structural database and identified 641 previously unrecognized Ankyrin repeat proteins. We observe a unique eigen spectra profile for different repeat types and show that the method can be easily extended to detect other repeat types. It is implemented as a web server, AnkPred. It is freely available at 'bioinf.iiit.ac.in/AnkPred'. AnkPred provides an elegant and

  15. Extremely stable all solution processed organic tandem solar cells with TiO2/GO recombination layer under continuous light illumination.

    PubMed

    Yusoff, Abd Rashid bin Mohd; Jose da Silva, Wilson; Kim, Hyeong Pil; Jang, Jin

    2013-11-21

    One approach to harvest a wide solar spectral solar energy is to stack two solar cells with different absorption characteristics in a tandem cell architecture. Herein, solution processed tandem solar cells, with highly transparent titanium oxide (TiO2) and graphene oxide (GO) as an efficient recombination layer, were designed, fabricated and characterized. We have adopted poly[(4,4'-bis(3-ethylhexyl)dithieno[3,2-b:''3'-d]silole)-2,6-diyl-alt-(2,5-(3-(2-ethylhexyl)thiophen-2-yl)thiazolo[5,4-d]thiazole]:indene-C60 bisadduct (PSEHTT:ICBA) and poly[(4,4'-bis(2-ethylhexyl)dithieno[3,2-b:2',3'-d]silole)-2,6-diyl-alt-(2,1,3-benzothiadiazole)-4,7-diyl]:[6,6]-phenyl-C70 butyric acid methyl ester (PSBTBT:PC70BM) as the active layers for the front and rear cells, respectively. The TiO2/GO serves as an electron and hole collecting and recombination layer. The tandem solar cells showed a high open circuit voltage (VOC) 1.62 V, a moderate short circuit current density (JSC) 8.23 mA cm(-2), fill factor (FF) 62.98%, leading to the power conversion efficiency of 8.40%. The obtained VOC value of tandem solar cells is ideal for the summation of VOCs attained from front and rear cells and it is evident that our tandem solar cells are well connected in series. Moreover, this tandem cell exhibits a 20% drop in conversion efficiency under continuous AM illumination for 2880 h.

  16. Dosimetric Comparison of Tandem and Ovoids vs. Tandem and Ring for Intracavitary Gynecologic Applications

    SciTech Connect

    Levin, Daphne Menhel, Janna; Rabin, Tanya; Pfeffer, M. Raphael; Symon, Zvi

    2008-01-01

    We evaluated dosimetric differences in tandem and ovoid (TO) and tandem and ring (TR) gynecologic brachytherapy applicators. Seventeen patients with cervical cancer (Stages II-IV) receiving 3 high-dose-rate (HDR) brachytherapy applications (both TO and TR) were studied. Patients underwent computed tomography (CT) scans with contrast in bladder, and were prescribed 8 Gy to ICRU points A, with additional optimization goals of maintaining the pear-shaped dose distribution and minimizing bladder and rectum doses. Bladder and rectum point doses, mean, and maximum doses were calculated. Total treatment time and volumes treated to 95%, 85%, 50%, and 20% or the prescription dose were compared. There were no significant differences between TO and TR applicators in doses to prescription points or critical organs. However, there were significant differences (p < 0.001) between the applicators in treated volumes and total treatment time. The TO treated larger volumes over a longer time. Within each patient, when the applicators were compared, treated volumes were also found to be significantly different (p < 0.01, {chi}{sup 2}). Our results demonstrate that the 2 applicators, while delivering the prescribed dose to points A and keeping critical organ doses below tolerance, treat significantly different volumes. It is unclear if this difference is clinically meaningful. TO applicators may be treating surrounding healthy tissue unnecessarily, or TR applicators may be underdosing tumor tissue. Further investigation with appropriate imaging modalities is required for accurate delineation of target volumes. Clearly, the TO and TR are not identical, and should not be used interchangeably without further study.

  17. Tandem repeats modify the structure of the canine CD1D gene.

    PubMed

    Looringh van Beeck, F A; Leegwater, P A J; Herrmann, T; Broere, F; Rutten, V P M G; Willemse, T; Van Rhijn, I

    2013-06-01

    Among the CD1 proteins that present lipid antigens to T cells, CD1d is the only one that stimulates a population of T cells with an invariant T-cell receptor known as NKT cells. Sequencing of a 722 nucleotide gap in the dog (Canis lupus familiaris) genome revealed that the canine CD1D gene lacks a sequence homologous to exon 2 of human CD1D, coding for the start codon and signal peptide. Also, the canine CD1D gene contains three different short tandem repeats that disrupt the expected gene structure. Because canine CD1D cDNA lacks sequences homologous to human exon 2 and 3, the functionality of canine CD1d protein may be affected, and this could have consequences for the development and activation of canine NKT cells.

  18. Additional testing of the inlets designed for a tandem fan V/STOL nacelle

    NASA Technical Reports Server (NTRS)

    Ybarra, A. H.

    1981-01-01

    The wind tunnel testing of a scale model of a tandem fan nacelle designed for a type (subsonic cruise) V/STOL aircraft configuration is discussed. The performance for the isolated front inlet and for the combined front and aft inlets is reported. Model variables include front and aft inlets with aft inlet variations of short and long aft inlet cowls, with a shaft simulator and diffuser vortex generators, cowl lip fillets, and nacelle strakes. Inlet pressure recovery, distortion, and inlet angle-to-attack separation limits were evaluated at tunnel velocity from 0 to 240 knots, angles-of-attack from -10 to +40 degrees and inlet flow rates corresponding to throat Mach number from 0.0 to 0.6. Combined nacelle pitch and yaw runs up to 30 deg. were also made.

  19. A new optically pumped tandem magnetometer: principles and experiences

    NASA Astrophysics Data System (ADS)

    Pulz, E.; Jäckel, K.-H.; Linthe, H.-J.

    1999-11-01

    In this paper we describe a new design for an optically pumped tandem magnetometer situated at the GeoForschungsZentrum Potsdam. A tandem magnetometer combines the fast response of a self-oscillating vapour magnetometer with the accuracy of a narrow line Mz-type magnetometer. A newly patented method of coupling the two sensors avoids any stray magnetic fields and so allows a compact design of the instrument itself, as well as facilitating its operation in close proximity to other magnetometers. A prototype Cs-K tandem magnetometer for use in magnetic observatories is described. We then show typical results of a long-term comparison with both a second type of optically pumped magnetometer and an Overhauser proton magnetometer. Finally, a resuméis given of four years of continuous operation of this new type of magnetometer with respect to the data quality produced and its operational reliability.

  20. High efficiency all-polymer tandem solar cells

    PubMed Central

    Yuan, Jianyu; Gu, Jinan; Shi, Guozheng; Sun, Jianxia; Wang, Hai-Qiao; Ma, Wanli

    2016-01-01

    In this work, we have reported for the first time an efficient all-polymer tandem cell using identical sub-cells based on P2F-DO:N2200. A high power conversion efficiency (PCE) of 6.70% was achieved, which is among the highest efficiencies for all polymer solar cells and 43% larger than the PCE of single junction cell. The largely improved device performance can be mainly attributed to the enhanced absorption of tandem cell. Meanwhile, the carrier collection in device remains efficient by optimizing the recombination layer and sub-cell film thickness. Thus tandem structure can become an easy approach to effectively boost the performance of current all polymer solar cells. PMID:27226354

  1. A tandem mirror plasma source for hybrid plume plasma studies

    NASA Technical Reports Server (NTRS)

    Yang, T. F.; Chang, F. R.; Miller, R. H.; Wenzel, K. W.; Krueger, W. A.

    1985-01-01

    A tandem mirror device to be considered as a hot plasma source for the hybrid plume rocket concept is discussed. The hot plamsa from this device is injected into an exhaust duct, which will interact with an annular hypersonic layer of neutral gas. The device can be used to study the dynamics of the hybrid plume, and to verify the numerical predictions obtained with computer codes. The basic system design is also geared towards low weight and compactness, and high power density at the exhaust. The basic structure of the device consists of four major subsystems: (1) an electric power supply; (2) a low temperature, high density plasma gun, such as a stream gun, an MPD source or gas cell; (3) a power booster in the form of a tandem mirror machine; and (4) an exhaust nozzle arrangement. The configuration of the tandem mirror section is shown.

  2. Tandem repeat distribution of gene transcripts in three plant families

    PubMed Central

    2009-01-01

    Tandem repeats (microsatellites or SSRs) are molecular markers with great potential for plant genetic studies. Modern strategies include the transfer of these markers among widely studied and orphan species. In silico analyses allow for studying distribution patterns of microsatellites and predicting which motifs would be more amenable to interspecies transfer. Transcribed sequences (Unigene) from ten species of three plant families were surveyed for the occurrence of micro and minisatellites. Transcripts from different species displayed different rates of tandem repeat occurrence, ranging from 1.47% to 11.28%. Both similar and different patterns were found within and among plant families. The results also indicate a lack of association between genome size and tandem repeat fractions in expressed regions. The conservation of motifs among species and its implication on genome evolution and dynamics are discussed. PMID:21637460

  3. Structural analysis of a multifunctional, tandemly repeated inositol polyphosphatase.

    PubMed

    Gruninger, Robert J; Selinger, L Brent; Mosimann, Steven C

    2009-09-11

    Mitsuokella multacida expresses a unique inositol polyphosphatase (PhyAmm) that is composed of tandem repeats (TRs). Each repeat possesses a protein tyrosine phosphatase (PTP) active-site signature sequence and fold. Using a combination of structural, mutational, and kinetic studies, we show that the N-terminal (D1) and C-terminal (D2) active sites of the TR have diverged and possess significantly different specificities for inositol polyphosphate. Structural analysis and molecular docking calculations identify steric and electrostatic differences within the substrate binding pocket of each TR that may be involved in the altered substrate specificity. The implications of our results for the biological function of related PTP-like phytases are discussed. Finally, the structures and activities of PhyAmm and tandemly repeated receptor PTPs are compared and discussed. To our knowledge, this is the first example of an inositol phosphatase with tandem PTP domains possessing substrate specificity for different inositol phosphates.

  4. A periodic table of symmetric tandem mismatches in RNA.

    PubMed

    Wu, M; McDowell, J A; Turner, D H

    1995-03-14

    The stabilities and structures of a series of RNA octamers containing symmetric tandem mismatches were studied by UV melting and imino proton NMR. The free energy increments for tandem mismatch formation are found to depend upon both mismatch sequence and adjacent base pairs. The observed sequence dependence of tandem mismatch stability is UGGU > GUUG > GAAG > or = AGGA > UUUU > CAAC > or = CUUC approximately UCCU approximately CCCC approximately ACCA approximately AAAA, and the closing base pair dependence is 5'G3'C > 5'C3'G > 5'U3'A approximately 5'A3'U. These results differ from expectations based on models used in RNA folding algorithms and from the sequence dependence observed for folding of RNA hairpins. Imino proton NMR results indicate the sequence dependence is partially due to hydrogen bonding within mismatches.

  5. A tandem mirror hybrid plume plasma propulsion facility

    NASA Technical Reports Server (NTRS)

    Yang, T. F.; Krueger, W. A.; Peng, S.; Urbahn, J.; Chang-Diaz, F. R.

    1988-01-01

    This paper discusses a novel concept in electrodeless plasma propulsion, in which the materials problems are ameliorated by an electrodeless magnetic confinement scheme borrowed from the tandem mirror approach to controlled thermonuclear fusion. The concept also features a two-stage magnetic nozzle with an annular hypersonic coaxial gas injector near the throat. The nozzle produces hybrid plume by the coaxial injection of hypersonic neutral gas, and the gas layer thus formed protects the material walls from the hot plasma and, through increased collisions, helps detach it from the diverging magnetic field. The tandem mirror plasma propulsion facility is capable of delivering a variable I(sp). The results of numerical simulation of this concept are presented together with those from an experimental tandem-mirror plasma propulsion device.

  6. Overall Photoelectrochemical Water Splitting using Tandem Cell under Simulated Sunlight.

    PubMed

    Kim, Jin Hyun; Kaneko, Hiroyuki; Minegishi, Tsutomu; Kubota, Jun; Domen, Kazunari; Lee, Jae Sung

    2016-01-08

    A stand-alone photoelectrochemical (PEC) water-splitting system driven only by sunlight was demonstrated with a tandem-scheme of Pt/CdS/CuGa3 Se5 /(Ag,Cu)GaSe2 photocathode and NiOOH/FeOOH/Mo:BiVO4 photoanode in a neutral phosphate buffer solution as an electrolyte. The as-prepared semi-transparent Mo:BiVO4 layer allows sunlight to pass through the top photoanode and reach the bottom photocathode. Consequently, the tandem cell showed stoichiometric hydrogen and oxygen evolution with a solar-to-hydrogen (STH) conversion efficiency of 0.67 % over 2 h without degradation. The stability and STH efficiency are the highest among similar configuration of PEC tandem cells. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Tandem photovoltaic solar cells and increased solar energy conversion efficiency

    NASA Technical Reports Server (NTRS)

    Loferski, J. J.

    1976-01-01

    Tandem photovoltaic cells, as proposed by Jackson (1955) to increase the efficiency of solar energy conversion, involve the construction of a system of stacked p/n homojunction photovoltaic cells composed of different semiconductors. It had been pointed out by critics, however, that the total power which could be extracted from the cells in the stack placed side by side was substantially greater than the power obtained from the stacked cells. A reexamination of the tandem cell concept in view of the development of the past few years is conducted. It is concluded that the use of tandem cell systems in flat plate collectors, as originally envisioned by Jackson, may yet become feasible as a result of the development of economically acceptable solar cells for large scale terrestrial power generation.

  8. Tandem photovoltaic solar cells and increased solar energy conversion efficiency

    NASA Technical Reports Server (NTRS)

    Loferski, J. J.

    1976-01-01

    Tandem photovoltaic cells, as proposed by Jackson (1955) to increase the efficiency of solar energy conversion, involve the construction of a system of stacked p/n homojunction photovoltaic cells composed of different semiconductors. It had been pointed out by critics, however, that the total power which could be extracted from the cells in the stack placed side by side was substantially greater than the power obtained from the stacked cells. A reexamination of the tandem cell concept in view of the development of the past few years is conducted. It is concluded that the use of tandem cell systems in flat plate collectors, as originally envisioned by Jackson, may yet become feasible as a result of the development of economically acceptable solar cells for large scale terrestrial power generation.

  9. mreps: efficient and flexible detection of tandem repeats in DNA

    PubMed Central

    Kolpakov, Roman; Bana, Ghizlane; Kucherov, Gregory

    2003-01-01

    The presence of repeated sequences is a fundamental feature of genomes. Tandemly repeated DNA appears in both eukaryotic and prokaryotic genomes, it is associated with various regulatory mechanisms and plays an important role in genomic fingerprinting. In this paper, we describe mreps, a powerful software tool for a fast identification of tandemly repeated structures in DNA sequences. mreps is able to identify all types of tandem repeats within a single run on a whole genomic sequence. It has a resolution parameter that allows the program to identify ‘fuzzy’ repeats. We introduce main algorithmic solutions behind mreps, describe its usage, give some execution time benchmarks and present several case studies to illustrate its capabilities. The mreps web interface is accessible through http://www.loria.fr/mreps/. PMID:12824391

  10. A tandem mirror plasma source for hybrid plume plasma studies

    NASA Technical Reports Server (NTRS)

    Yang, T. F.; Chang, F. R.; Miller, R. H.; Wenzel, K. W.; Krueger, W. A.

    1985-01-01

    A tandem mirror device to be considered as a hot plasma source for the hybrid plume rocket concept is discussed. The hot plamsa from this device is injected into an exhaust duct, which will interact with an annular hypersonic layer of neutral gas. The device can be used to study the dynamics of the hybrid plume, and to verify the numerical predictions obtained with computer codes. The basic system design is also geared towards low weight and compactness, and high power density at the exhaust. The basic structure of the device consists of four major subsystems: (1) an electric power supply; (2) a low temperature, high density plasma gun, such as a stream gun, an MPD source or gas cell; (3) a power booster in the form of a tandem mirror machine; and (4) an exhaust nozzle arrangement. The configuration of the tandem mirror section is shown.

  11. Highly Loaded Fan by Using Tandem Cascade Rotor Blade

    NASA Astrophysics Data System (ADS)

    Hasegawa, Hiroaki; Suga, Shinya; Matsuoka, Akinori

    For axial flow compressors and fans in the aircraft engines higher pressure ratio is required in order to attain the high thrust engines. In this study, the fan with the tandem cascades was introduced to increase the fan pressure ratio. The use of tandem cascades in the fan allows savings in length and weight and therefore a compact fan could be built. The design of fan with tandem cascades and the fan testing were carried out to develop the high pressure ratio fan for the Air Turbo Ramjet (ATR) propulsion system. The ATR is a combined cycle engine which performs like a turbojet engine at subsonic speeds and a ramjet at supersonic speeds. In particular, high fan pressure ratio contributes to increase the engine thrust during subsonic flight at which the engine does not make use of ram effect. The results of the fan testing indicate that the pressure ratio of 2.2 is achieved in single stage fan.

  12. Unsteady Flowfield Around Tandem Cylinders as Prototype for Component Interaction in Airframe Noise

    NASA Technical Reports Server (NTRS)

    Khorrami, Meldi R.; Choudhari, Meelan M.; Jenkins, Luther N.; McGinley, Catherine B.

    2005-01-01

    Synergistic application of experiments and numerical simulations is crucial to understanding the underlying physics of airframe noise sources. The current effort is aimed at characterizing the details of the flow interaction between two cylinders in a tandem configuration. This setup is viewed to be representative of several component-level flow interactions that occur when air flows over the main landing gear of large civil transports. Interactions of this type are likely to have a significant impact on the noise radiation associated with the aircraft undercarriage. The paper is focused on two-dimensional, time-accurate flow simulations for the tandem cylinder configuration. Results of the unsteady Reynolds Averaged Navier-Stokes (URANS) computations with a two-equation turbulence model, at a Reynolds number of 0.166 million and a Mach number of 0.166, are presented. The experimental measurements of the same flow field are discussed in a separate paper by Jenkins, Khorrami, Choudhari, and McGinley (2005). Two distinct flow regimes of interest, associated with short and intermediate separation distances between the two cylinders, are considered. Emphasis is placed on understanding both time averaged and unsteady flow features between the two cylinders and in the wake of the rear cylinder. Predicted mean flow quantities and vortex shedding frequencies show reasonable agreement with the measured data for both cylinder spacings. Computations for short separation distance indicate decay of flow unsteadiness with time, which is not unphysical; however, the predicted sensitivity of mean lift coefficient to small angles of attack explains the asymmetric flowfield observed during the experiments.

  13. Summary of the MARS tandem-mirror reactor design

    SciTech Connect

    Logan, B.G.

    1983-09-01

    A recently completed two-year study of a commercial tandem-mirror reactor design (Mirror Advanced Reactor Study (MARS)) is briefly reviewed. The end plugs are designed for trapped-particle stability, MHD ballooning, balanced geodesic curvature, and small radial electric fields in the central cell. New technologies such as lithium-lead blankets, 24 T hybrid coils, gridless direct converters and plasma halo vacuum pumps are highlighted. General characteristics of the MARS tandem mirror and STARFIRE tokamak reactor design are compared. A design of an upgrade of MFTF-B incorporating many of the MARS features is discussed.

  14. Tandem riboswitch architectures exhibit complex gene control functions.

    PubMed

    Sudarsan, Narasimhan; Hammond, Ming C; Block, Kirsten F; Welz, Rüdiger; Barrick, Jeffrey E; Roth, Adam; Breaker, Ronald R

    2006-10-13

    Riboswitches are structured RNAs typically located in the 5' untranslated regions of bacterial mRNAs that bind metabolites and control gene expression. Most riboswitches sense one metabolite and function as simple genetic switches. However, we found that the 5' region of the Bacillus clausii metE messenger RNA includes two riboswitches that respond to S-adenosylmethionine and coenzyme B12. This tandem arrangement yields a composite gene control system that functions as a two-input Boolean NOR logic gate. These findings and the discovery of additional tandem riboswitch architectures reveal how simple RNA elements can be assembled to make sophisticated genetic decisions without involving protein factors.

  15. Short synthesis of ethyl 3-(3-aminophenyl)propanoate.

    PubMed

    Nagel, Ulrike; Radau, Gregor; Link, Andreas

    2011-12-01

    A short and effective synthesis of ethyl 3-(3-aminophenyl)propanoate is presented, employing a tandem Knoevenagel condensation/alkylidene reduction of 3-nitrobenzaldehyde with Meldrum's acid in TEAF (triethylammonium formate) followed by reduction of the intermediate 3-(3-nitrophenyl)propanoic acid by stannous chloride in ethanol. The use of stannous chloride as the reducing agent in ethanol enabled the simultaneous esterification of the carboxylic acid. Thus, stannous chloride was acting simultaneously as a Lewis acid, which activates the carboxylic acid towards a nucleophilic attack by ethanol.

  16. Paediatric short case examination.

    PubMed

    Isaacs, David

    2014-11-01

    The short case is a highly artificial scenario, in which the examination candidate is given little or no history and instructed to examine one system or one aspect of a patient and draw conclusions. Despite their artificiality, short cases test clinical skills which senior paediatricians value and consider essential qualities of a competent physician. This article presents some general suggestions on an approach to doing short case examinations.

  17. Performance of a tandem-rotor/tandem-stator conical-flow compressor designed for a pressure ratio of 3

    NASA Technical Reports Server (NTRS)

    Wood, J. R.; Owen, A. K.; Schumann, L. F.

    1982-01-01

    A conical-flow compressor stage with a large radius change through the rotor was tested at three values of rotor tip clearance. The stage had a tandem rotor and a tandem stator. Peak efficiency at design speed was 0.774 at a pressure ratio of 2.613. The rotor was tested without the stator, and detailed survey data were obtained for each rotor blade row. Overall peak rotor efficiency was 0.871 at a pressure ratio of 2.952.

  18. Development of high band gap materials for tandem solar cells and simulation studies on mechanical tandem solar cells

    NASA Astrophysics Data System (ADS)

    Vijayakumar, Vishnuvardhanan

    Development of low cost, high efficiency tandem solar cells is essential for large scale adoption of solar energy especially in densely populated regions of the world. In this thesis four-terminal mechanical (stack like) tandem solar cells were evaluated using detailed simulation models and design criteria for selecting candidate materials were established. Since silicon solar cells are low cost and have a multi-giga watt global manufacturing and supply chain capacity already in place then only tandem stacks incorporating silicon as one of the layers in the device was investigated. Two candidate materials which have high band gaps that could be used as top cells in the mechanical tandem device were explored as part of the thesis. Dye-sensitized solar cells (DSSC) sensitized with N719 dye (one of the candidates for the top cell) were fabricated with the goal of enabling a flexible processing path to lower cost. Stainless steel (SS) mesh substrates were used to fabricate anodes for flexible DSSC in order to evaluate them as replacements for more expensive Transparent Conducting Oxides (TCO's). Loss mechanisms in DSSC's due to SS mesh oxidation were quantified and protective coatings to prevent oxidation of SS mesh were developed. The second material which was evaluated for use as the top cell was copper zinc tin sulfide (CZTS). CZTS was deposited through a solution deposition route. Detailed investigations were done on the deposited films to understand the chemistry, crystal structure and its opto-electronic properties. Deposited CZTS films were found to be highly crystalline in <112> direction. The films had a direct band gap of 1.5 eV with absorption coefficient greater than 104 cm -1 in agreement with published values. In the second part of the thesis detailed electrical and optical simulation models of the mechanical tandem solar cells were developed based on the most up-to-date materials physical constants available for each layer. The modeling was used to

  19. Low-bandgap mixed tin-lead iodide perovskite absorbers with long carrier lifetimes for all-perovskite tandem solar cells

    NASA Astrophysics Data System (ADS)

    Zhao, Dewei; Yu, Yue; Wang, Changlei; Liao, Weiqiang; Shrestha, Niraj; Grice, Corey R.; Cimaroli, Alexander J.; Guan, Lei; Ellingson, Randy J.; Zhu, Kai; Zhao, Xingzhong; Xiong, Ren-Gen; Yan, Yanfa

    2017-03-01

    Tandem solar cells using only metal-halide perovskite sub-cells are an attractive choice for next-generation solar cells. However, the progress in developing efficient all-perovskite tandem solar cells has been hindered by the lack of high-performance low-bandgap perovskite solar cells. Here, we report efficient mixed tin-lead iodide low-bandgap (˜1.25 eV) perovskite solar cells with open-circuit voltages up to 0.85 V and over 70% external quantum efficiencies in the infrared wavelength range of 700-900 nm, delivering a short-circuit current density of over 29 mA cm-2 and demonstrating suitability for bottom-cell applications in all-perovskite tandem solar cells. Our low-bandgap perovskite solar cells achieve a maximum power conversion efficiency of 17.6% and a certified efficiency of 17.01% with a negligible current-voltage hysteresis. When mechanically stacked with a ˜1.58 eV bandgap perovskite top cell, our best all-perovskite 4-terminal tandem solar cell shows a steady-state efficiency of 21.0%.

  20. Allele-specific transcriptional activity of the variable number of tandem repeats in 5' region of the DRD4 gene is stimulus specific in human neuronal cells.

    PubMed

    Paredes, U M; Quinn, J P; D'Souza, U M

    2013-03-01

    The dopamine receptor D4 (DRD4) gene includes several variable number of tandem repeat loci that have been suggested to modulate DRD4 gene expression patterns. Previous studies showed differential basal activity of the two most common variants of a tandem repeat (120 bp per repeat unit) located in the 5' region adjacent to the DRD4 promoter in human cell lines. In this communication, we further characterized the ability of this polymorphic repeat to elicit tissue-, allele- and stimuli-specific transcriptional activity in vitro. The short and long variants of the DRD4 5' tandem repeat were cloned into a luciferase reporter gene construct containing the SV40 promoter. The luciferase constructs were cotransfected with expression vectors of two ubiquitously expressed human transcription factors (TFs), CCCTC-binding factor (CTCF) and upstream stimulatory factor 2 (USF2), into human cell lines and primary cultures of neonate rat cortex and luciferase activity measured. Overexpression with these TFs resulted in differential cell- and allele-specific transcriptional activities of the luciferase constructs. The results of our experiments show that variants of this tandem repeat in the 5' promoter of the DRD4 gene will direct differential reporter gene transcriptional activity in a cell-type-specific manner dependent on the signal pathways activated.

  1. 14 CFR 105.45 - Use of tandem parachute systems.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...) Has completed a minimum of 500 freefall parachute jumps using a ram-air parachute, and (iii) Holds a... parachute jump with a tandem parachute system unless— (1) The main parachute has been packed by a certificated parachute rigger, the parachutist in command making the next jump with that parachute, or a...

  2. Robust Decentralized Detection and Social Learning in Tandem Networks

    NASA Astrophysics Data System (ADS)

    Ho, Jack; Tay, Wee Peng; Quek, Tony Q. S.; Chong, Edwin K. P.

    2015-10-01

    We study a tandem of agents who make decisions about an underlying binary hypothesis, where the distribution of the agent observations under each hypothesis comes from an uncertainty class. We investigate both decentralized detection rules, where agents collaborate to minimize the error probability of the final agent, and social learning rules, where each agent minimizes its own local minimax error probability. We then extend our results to the infinite tandem network, and derive necessary and sufficient conditions on the uncertainty classes for the minimax error probability to converge to zero when agents know their positions in the tandem. On the other hand, when agents do not know their positions in the network, we study the cases where agents collaborate to minimize the asymptotic minimax error probability, and where agents seek to minimize their worst-case minimax error probability (over all possible positions in the tandem). We show that asymptotic learning of the true hypothesis is no longer possible in these cases, and derive characterizations for the minimax error performance.

  3. Tandem warhead considerations for electronic safety and arming devices

    SciTech Connect

    Dell, D.; Medina, A.

    1990-01-01

    There are four issues that an ESA designer must address when designing a tandem system: (1) warhead detonation shock, (2) warhead detonation ion cloud, (3) warhead detonation electromagnetic pulse, and (4) slapper/sparkgap electromagnetic pulse. Each of these hazards can upset the ESA time delay circuitry which would then either dud the munition or prematurely detonate the main charge. 14 figs.

  4. The Dynamics of Social Interaction in Telecollaborative Tandem Exchanges

    ERIC Educational Resources Information Center

    Janssen Sanchez, Brianna

    2015-01-01

    Using both quantitative and qualitative methods of inquiry, this dissertation study undertakes an exploration of the dynamics of the social interaction in discourse co-constructed by pairs of college students in telecollaborative tandem exchanges. Two groups of participants, Mexican learners of English as a foreign language and American learners…

  5. High efficiency GaAs/Ge monolithic tandem solar cells

    NASA Technical Reports Server (NTRS)

    Tobin, S. P.; Vernon, S. M.; Bajgar, C.; Haven, V. E.; Geoffroy, L. M.; Sanfacon, M. M.; Lillington, D. R.; Hart, R. E., Jr.

    1988-01-01

    Two-terminal monolithic tandem cells consisting of a GaAs solar cell grown epitaxially on a Ge solar cell substrate are very attractive for space applications. Tandem cells of GaAs grown by metal-organic chemical vapor deposition on thin Ge were investigated to address both higher efficiency and reduced weight. Two materials growth issues associated with this heteroepitaxial system, autodoping of the GaAs layers by Ge and diffusion of Ga and As into the Ge substrate, were addressed. The latter appears to result in information of an unintentional p-n junction in the Ge. Early simulator measurements gave efficiencies as high as 21.7 percent for 4 cm2 GaAs/Ge cells, but recent high-altitude testing has given efficiencies of 18 percent. Sources of errors in simulator measurements of two-terminal tandem cells are discussed. A limiting efficiency of about 36 percent for the tandem cell at AMO was calculated. Ways to improve the performance of present cells, primarily by increasing the Isc and Voc of the Ge cell, are proposed.

  6. Bio-olefins from unsaturated fatty acids via tandem catalysis

    USDA-ARS?s Scientific Manuscript database

    A new catalytic route to bio-olefins from unsaturated fatty acids will be described. At the heart of the process, the catalyst apparently functions in a tandem mode by both dynamically isomerizing the positions of double bonds in an aliphatic chain and, subsequently, decarboxylating specific isomers...

  7. Dynamics of tandem bubble interaction in a microfluidic channel

    PubMed Central

    Yuan, Fang; Sankin, Georgy; Zhong, Pei

    2011-01-01

    The dynamics of tandem bubble interaction in a microfluidic channel (800 × 21 μm, W × H) have been investigated using high-speed photography, with resultant fluid motion characterized by particle imaging velocimetry. A single or tandem bubble is produced reliably via laser absorption by micron-sized gold dots (6 μm in diameter with 40 μm in separation distance) coated on a glass surface of the microfluidic channel. Using two pulsed Nd:YAG lasers at λ = 1064 nm and ∼10 μJ/pulse, the dynamics of tandem bubble interaction (individual maximum bubble diameter of 50 μm with a corresponding collapse time of 5.7 μs) are examined at different phase delays. In close proximity (i.e., interbubble distance = 40 μm or γ = 0.8), the tandem bubbles interact strongly with each other, leading to asymmetric deformation of the bubble walls and jet formation, as well as the production of two pairs of vortices in the surrounding fluid rotating in opposite directions. The direction and speed of the jet (up to 95 m/s), as well as the orientation and strength of the vortices can be varied by adjusting the phase delay. PMID:22088007

  8. Dynamics of tandem bubble interaction in a microfluidic channel.

    PubMed

    Yuan, Fang; Sankin, Georgy; Zhong, Pei

    2011-11-01

    The dynamics of tandem bubble interaction in a microfluidic channel (800  ×  21 μm, W × H) have been investigated using high-speed photography, with resultant fluid motion characterized by particle imaging velocimetry. A single or tandem bubble is produced reliably via laser absorption by micron-sized gold dots (6 μm in diameter with 40 μm in separation distance) coated on a glass surface of the microfluidic channel. Using two pulsed Nd:YAG lasers at λ = 1064 nm and ∼10 μJ/pulse, the dynamics of tandem bubble interaction (individual maximum bubble diameter of 50 μm with a corresponding collapse time of 5.7 μs) are examined at different phase delays. In close proximity (i.e., interbubble distance = 40 μm or γ = 0.8), the tandem bubbles interact strongly with each other, leading to asymmetric deformation of the bubble walls and jet formation, as well as the production of two pairs of vortices in the surrounding fluid rotating in opposite directions. The direction and speed of the jet (up to 95 m/s), as well as the orientation and strength of the vortices can be varied by adjusting the phase delay.

  9. High efficiency GaAs/Ge monolithic tandem solar cells

    NASA Technical Reports Server (NTRS)

    Tobin, S. P.; Vernon, S. M.; Bajgar, C.; Haven, V. E.; Geoffroy, L. M.; Sanfacon, M. M.; Lillington, D. R.; Hart, R. E., Jr.

    1988-01-01

    Two-terminal monolithic tandem cells consisting of a GaAs solar cell grown epitaxially on a Ge solar cell substrate are very attractive for space applications. Tandem cells of GaAs grown by metal-organic chemical vapor deposition on thin Ge were investigated to address both higher efficiency and reduced weight. Two materials growth issues associated with this heteroepitaxial system, autodoping of the GaAs layers by Ge and diffusion of Ga and As into the Ge substrate, were addressed. The latter appears to result in information of an unintentional p-n junction in the Ge. Early simulator measurements gave efficiencies as high as 21.7 percent for 4 cm2 GaAs/Ge cells, but recent high-altitude testing has given efficiencies of 18 percent. Sources of errors in simulator measurements of two-terminal tandem cells are discussed. A limiting efficiency of about 36 percent for the tandem cell at AMO was calculated. Ways to improve the performance of present cells, primarily by increasing the Isc and Voc of the Ge cell, are proposed.

  10. Optochemokine Tandem for Light-Control of Intracellular Ca2+

    PubMed Central

    Weissbecker, Juliane; Sauer, Frank; Wood, Phillip G.; Bamberg, Ernst

    2016-01-01

    An optochemokine tandem was developed to control the release of calcium from endosomes into the cytosol by light and to analyze the internalization kinetics of G-protein coupled receptors (GPCRs) by electrophysiology. A previously constructed rhodopsin tandem was re-engineered to combine the light-gated Ca2+-permeable cation channel Channelrhodopsin-2(L132C), CatCh, with the chemokine receptor CXCR4 in a functional tandem protein tCXCR4/CatCh. The GPCR was used as a shuttle protein to displace CatCh from the plasma membrane into intracellular areas. As shown by patch-clamp measurements and confocal laser scanning microscopy, heterologously expressed tCXCR4/CatCh was internalized via the endocytic SDF1/CXCR4 signaling pathway. The kinetics of internalization could be followed electrophysiologically via the amplitude of the CatCh signal. The light-induced release of Ca2+ by tandem endosomes into the cytosol via CatCh was visualized using the Ca2+-sensitive dyes rhod2 and rhod2-AM showing an increase of intracellular Ca2+ in response to light. PMID:27768773

  11. Design considerations for the Tandem Junction Solar Cell

    NASA Technical Reports Server (NTRS)

    Matzen, W. T.; Carbajal, B. G.; Hardy, R. W.

    1979-01-01

    Structure and operation of the tandem junction cell (TJC) are described. The impact of using only back contacts is discussed. A model is presented which explains operation of the TJC in terms of transistor action. The model is applied to predict TJC performance as a function of physical parameters.

  12. Interpretation of tandem mass spectra of posttranslationally modified peptides.

    PubMed

    Bunkenborg, Jakob; Matthiesen, Rune

    2013-01-01

    Tandem mass spectrometry provides a sensitive means of analyzing the amino acid sequence of peptides and modified peptides by providing accurate mass measurements of precursor and fragment ions. Modern mass spectrometry instrumentation is capable of rapidly generating many thousands of tandem mass spectra and protein database search engines have been developed to match the experimental data to peptide candidates. In most studies there is a schism between discarding perfectly valid data and including nonsensical peptide identifications-this is currently a major bottleneck in data-analysis and it calls for an understanding of tandem mass spectrometry data. Manual evaluation of the data and perhaps experimental cross-checking of the MS data can save many months of experimental work trying to do biological follow-ups based on erroneous identifications. Especially for posttranslationally modified peptides there is a need for manual validation of the data because search algorithms seldom have been optimized for the identification of modified peptides and because there are many pitfalls for the unwary. This chapter describes some of the issues that should be considered when interpreting and validating tandem mass spectra and gives some useful tables to aid this process.

  13. High power tandem-pumped thulium-doped fiber laser.

    PubMed

    Wang, Yao; Yang, Jianlong; Huang, Chongyuan; Luo, Yongfeng; Wang, Shiwei; Tang, Yulong; Xu, Jianqiu

    2015-02-09

    We propose a cascaded tandem pumping technique and show its high power and high efficient operation in the 2-μm wavelength region, opening up a new way to scale the output power of the 2-μm fiber laser to new levels (e.g. 10 kW). Using a 1942 nm Tm(3+) fiber laser as the pump source with the co- (counter-) propagating configuration, the 2020 nm Tm(3+) fiber laser generates 34.68 W (35.15W) of output power with 84.4% (86.3%) optical-to-optical efficiency and 91.7% (92.4%) slope efficiency, with respect to launched pump power. It provides the highest slope efficiency reported for 2-μm Tm(3+)-doped fiber lasers, and the highest output power for all-fiber tandem-pumped 2-μm fiber oscillators. This system fulfills the complete structure of the proposed cascaded tandem pumping technique in the 2-μm wavelength region (~1900 nm → ~1940 nm → ~2020 nm). Numerical analysis is also carried out to show the power scaling capability and efficiency of the cascaded tandem pumping technique.

  14. ORIC stripping foil positioner for tandem beam injection

    SciTech Connect

    Ludemann, C.A.; Lord, R.S.; Hudson, E.D.; Irwin, F.; Beckers, R.M.; Haynes, D.L.; Casstevens, B.J.; Mosko, S.W.

    1981-01-01

    The Oak Ridge Isochronous Cyclotron (ORIC) is used as an energy booster for heavy ions from a 25 MV tandem accelerator. This operation requires precise placement of a stripping foil in the cyclotron for capture of the injected ions into an acceleration orbit. The mechanical design and control of the foil positioning device are described.

  15. Production of Arq+ ions with a tandem linear Paul trap

    NASA Astrophysics Data System (ADS)

    Higaki, H.; Nagayasu, K.; Iwai, T.; Ito, K.; Okamoto, H.

    2015-06-01

    A tandem linear Paul trap was used to create highly charged Argon ions by electron impact ionizations. By improving the operation scheme, the production of Ar4+ ions was confirmed. Possible improvements for the future experiments with laser cooled Ca+ ions are suggested.

  16. Tandem Fan Applications in Advanced STOVL Fighter Configurations

    NASA Technical Reports Server (NTRS)

    Zola, Charlse L.; Wilson, Samuel B., III; Eskey, Megan A.

    1984-01-01

    The series/parallel tandem fan engine is evaluated for application in advanced STOVL supersonic fighter aircraft. Options in engine cycle parameters and design of the front fan flow diverter are examined for their effects on engine weight, dimensions, and other factors in integration of the engine with the aircraft. Operation of the engine in high-bypass flow mode during cruise and loiter flight is considered as a means of minimizizng fuel consumption. Engine thrust augmentation by burning in the front fan exhaust is discussed. Achievement of very sort takeoff with vectored thrust in briefly reviewed for tandem fan engine configurations with vectorable front fan nozzles. Examples are given of two aircraft configuration planforms, a delta-canard, and a forward-swept wing, to illustrate the major features. design considerations, and potential performance of the tandem fan installation in each. Full realization of the advantages of tandem fan propulsion are found to depend on careful selection of the aircraft configuration, since integration requirements can strongly influence the engine performance.

  17. The "Bologna-München" Tandem--Experiencing Interculturality

    ERIC Educational Resources Information Center

    De Martino, Sandro

    2016-01-01

    This case study describes the "Bologna-München" Tandem, a cross-border collaboration which began in 2011. The aim of the collaboration is to give students studying Italian at the Ludwig- Maximilians-University in Munich and students studying German at the University of Bologna the opportunity to experience interculturality through…

  18. Propulsion Research on the Variable Tandem Mirror Plasma Rocket.

    DTIC Science & Technology

    1994-02-07

    T.F. Yang. and F.R. Chang-Diaz. An icrh beach effect in a tandem mirror device. To be submitted to Physics of Fluid. 9; Scott Peng, , J. Freidberg ...mirror plasma propulsion device. Technical Report To be Published, MIT Plasma Fusion Center, 1990. 14j J. F. Freidberg . Ideal magnetohydrodynamic theory

  19. PCR-free digital minisatellite tandem repeat genotyping.

    PubMed

    Chen, Yuchao; Seo, Tae Seok

    2011-06-01

    We demonstrated a proof-of-concept for novel minisatellite tandem repeat typing, called PCR-free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead-based solid-phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16-bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin-coated magnetic beads. After a denaturing step, a large amount of ligated products whose size difference was equivalent to the repeat unit were released and recovered. Through the elongated sample stacking μCE separation on a microdevice, the fluorescence signal of the ligated products was generated in the electropherogram and the peak number was directly counted which was exactly matched with the repeat number of VNTR locus. We could successfully identify the minisatellite tandem repeat number with only 5 fmol of DNA template in 30 min.

  20. The Dynamics of Social Interaction in Telecollaborative Tandem Exchanges

    ERIC Educational Resources Information Center

    Janssen Sanchez, Brianna

    2015-01-01

    Using both quantitative and qualitative methods of inquiry, this dissertation study undertakes an exploration of the dynamics of the social interaction in discourse co-constructed by pairs of college students in telecollaborative tandem exchanges. Two groups of participants, Mexican learners of English as a foreign language and American learners…

  1. II-IV-V Based Thin Film Tandem Photovoltaic Cell

    SciTech Connect

    Newman, Nathan; van Schilfgaarde, Mark

    2012-10-04

    [Through a combination of theory and experiment that, absent unknown mitigating factors, a tandem cell whose (wide-gap. 1.8 eV) top layer is made of ZnSnP2 and whose (narrow gap, 1.1 eV) bottom layer consisting of ZnGeAs2 are near-ideal materials for a tandem cell. Not only are there gaps optimally adjusted to the solar spectrum, but the two compounds are lattice-matched, and their energy band structure and optical absorption are also near-ideal (they closely resemble that of GaAs). Our first major challenge is to establish that high-quality II-IV-V thin films can be synthesized. We have begun growing and characterizing films of ZnGeAs2 and ZnSnP2, initially grown on Ge substrates (the lattice constant of Ge matches these compounds) by pulsed laser ablation and sputtering. In tandem are theoretical calculations to guide the experiments. The goal is to develop methods that can be used to produce a pair of lattice-matched thin films that will be useful in tandem cells.

  2. Development of an advanced spacecraft tandem mass spectrometer

    NASA Technical Reports Server (NTRS)

    Drew, Russell C.

    1992-01-01

    The purpose of this research was to apply current advanced technology in electronics and materials to the development of a miniaturized Tandem Mass Spectrometer that would have the potential for future development into a package suitable for spacecraft use. The mass spectrometer to be used as a basis for the tandem instrument would be a magnetic sector instrument, of Nier-Johnson configuration, as used on the Viking Mars Lander mission. This instrument configuration would then be matched with a suitable second stage MS to provide the benefits of tandem MS operation for rapid identification of unknown organic compounds. This tandem instrument is configured with a newly designed GC system to aid in separation of complex mixtures prior to MS analysis. A number of important results were achieved in the course of this project. Among them were the development of a miniaturized GC subsystem, with a unique desorber-injector, fully temperature feedback controlled oven with powered cooling for rapid reset to ambient conditions, a unique combination inlet system to the MS that provides for both membrane sampling and direct capillary column sample transfer, a compact and ruggedized alignment configuration for the MS, an improved ion source design for increased sensitivity, and a simple, rugged tandem MS configuration that is particularly adaptable to spacecraft use because of its low power and low vacuum pumping requirements. The potential applications of this research include use in manned spacecraft like the space station as a real-time detection and warning device for the presence of potentially harmful trace contaminants of the spacecraft atmosphere, use as an analytical device for evaluating samples collected on the Moon or a planetary surface, or even use in connection with monitoring potentially hazardous conditions that may exist in terrestrial locations such as launch pads, environmental test chambers or other sensitive areas. Commercial development of the technology

  3. Full Color Generation Using Silver Tandem Nanodisks.

    PubMed

    Wang, Hao; Wang, Xiaolong; Yan, Chen; Zhao, Hua; Zhang, Jingwen; Santschi, Christian; Martin, Olivier J F

    2017-03-27

    Plasmonic effects associated with metallic nanostructures have been widely studied for color generation. It became apparent that highly saturated and bright colors are hard to obtain, and very small nanostructures need to be fabricated. To address this issue, in this study, we employ metal-insulator-metal sandwich nanodisks that support enhanced in-phase electric dipole modes, which are blue-shifted with respect to a single metal disk. The blue shift enables the generation of short wavelength colors with larger nanostructures. The radiation modes hybridize with the Wood's anomaly in periodic structures, creating narrow and high-resonance peaks in the reflection and deep valleys in the transmission spectra, thus producing vivid complementary colors in both cases. Full colors can be achieved by tuning the radius of the nanodisks and the periodicity of the arrays. Good agreement between simulations and experiments is demonstrated and analyzed in CIE1931, sRGB, and HSV color spaces. The presented method has potential for applications in imaging, data storage, ultrafine displays, and plasmon-based biosensors.

  4. Large tandem repeats make up the chromosome bar code: a hypothesis.

    PubMed

    Podgornaya, Olga; Gavrilova, Ekaterina; Stephanova, Vera; Demin, Sergey; Komissarov, Aleksey

    2013-01-01

    Much of tandem repeats' functional nature in any genome remains enigmatic because there are only few tools available for dissecting and elucidating the functions of repeated DNA. The large tandem repeat arrays (satellite DNA) found in two mouse whole-genome shotgun assemblies were classified into 4 superfamilies, 8 families, and 62 subfamilies. With the simplified variant of chromosome positioning of different tandem repeats, we noticed the nonuniform distribution instead of the positions reported for mouse major and minor satellites. It is visible that each chromosome possesses a kind of unique code made up of different large tandem repeats. The reference genomes allow marking only internal tandem repeats, and even with such a limited data, the colored "bar code" made up of tandem repeats is visible. We suppose that tandem repeats bare the mechanism for chromosomes to recognize the regions to be associated. The associations, initially established via RNA, become fixed by histone modifications (the histone or chromatin code) and specific proteins. In such a way, associations, being at the beginning flexible and regulated, that is, adjustable, appear as irreversible and inheritable in cell generations. Tandem repeat multiformity tunes the developed nuclei 3D pattern by sequential steps of associations. Tandem repeats-based chromosome bar code could be the carrier of the genome structural information; that is, the order of precise tandem repeat association is the DNA morphogenetic program. Tandem repeats are the cores of the distinct 3D structures postulated in "gene gating" hypothesis. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Improving organic tandem solar cells based on water-processed nanoparticles by quantitative 3D nanoimaging

    NASA Astrophysics Data System (ADS)

    Pedersen, E. B. L.; Angmo, D.; Dam, H. F.; Thydén, K. T. S.; Andersen, T. R.; Skjønsfjell, E. T. B.; Krebs, F. C.; Holler, M.; Diaz, A.; Guizar-Sicairos, M.; Breiby, D. W.; Andreasen, J. W.

    2015-08-01

    Organic solar cells have great potential for upscaling due to roll-to-roll processing and a low energy payback time, making them an attractive sustainable energy source for the future. Active layers coated with water-dispersible Landfester particles enable greater control of the layer formation and easier access to the printing industry, which has reduced the use of organic solvents since the 1980s. Through ptychographic X-ray computed tomography (PXCT), we image quantitatively a roll-to-roll coated photovoltaic tandem stack consisting of one bulk heterojunction active layer and one Landfester particle active layer. We extract the layered morphology with structural and density information including the porosity present in the various layers and the silver electrode with high resolution in 3D. The Landfester particle layer is found to have an undesired morphology with negatively correlated top- and bottom interfaces, wide thickness distribution and only partial surface coverage causing electric short circuits through the layer. By top coating a polymer material onto the Landfester nanoparticles we eliminate the structural defects of the layer such as porosity and roughness, and achieve the increased performance larger than 1 V expected for a tandem cell. This study highlights that quantitative imaging of weakly scattering stacked layers of organic materials has become feasible by PXCT, and that this information cannot be obtained by other methods. In the present study, this technique specifically reveals the need to improve the coatability and layer formation of Landfester nanoparticles, thus allowing improved solar cells to be produced.Organic solar cells have great potential for upscaling due to roll-to-roll processing and a low energy payback time, making them an attractive sustainable energy source for the future. Active layers coated with water-dispersible Landfester particles enable greater control of the layer formation and easier access to the printing

  6. Short pulse test set

    NASA Astrophysics Data System (ADS)

    1990-11-01

    This report discusses the construction and operation of the Short Pulse Test Set that has been built for the U.S. Army Missile Command for the purpose of applying short (25 to 100 nanosecond), high voltage pulses to electronic explosive devices (EEDs) in both the pin-to-pin and pins-to-case mode. The test set employs the short pulse generating techniques first described in the Franklin Institute Research Laboratories (now Franklin Research Center) Report I-C3410, 'Pins-to-Case Short Pulse Sensitivity Studies for the Atlas DC Switch', December 1974. This report, authored by Ramie H. Thompson, was prepared for Picatinny Arsenal under contract DAAA21-72C-0766. The test set described herein utilizes a computer controlled high speed digitizer to monitor the pulse voltage and current and provides software to process and display these data.

  7. DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA).

    PubMed

    Jensen, Ronald W; Rivest, Jason; Li, Wei; Vissa, Varalakshmi

    2011-07-15

    The study of the transmission of leprosy is particularly difficult since the causative agent, Mycobacterium leprae, cannot be cultured in the laboratory. The only sources of the bacteria are leprosy patients, and experimentally infected armadillos and nude mice. Thus, many of the methods used in modern epidemiology are not available for the study of leprosy. Despite an extensive global drug treatment program for leprosy implemented by the WHO, leprosy remains endemic in many countries with approximately 250,000 new cases each year. The entire M. leprae genome has been mapped and many loci have been identified that have repeated segments of 2 or more base pairs (called micro- and minisatellites). Clinical strains of M. leprae may vary in the number of tandem repeated segments (short tandem repeats, STR) at many of these loci. Variable number tandem repeat (VNTR) analysis has been used to distinguish different strains of the leprosy bacilli. Some of the loci appear to be more stable than others, showing less variation in repeat numbers, while others seem to change more rapidly, sometimes in the same patient. While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing, the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. Multiple locus VNTR analysis (MLVA) has been used to study leprosy evolution and transmission in several countries including China, Malawi, the Philippines, and Brazil. MLVA involves multiple steps. First, bacterial DNA is extracted along with host tissue DNA from clinical biopsies or slit skin smears (SSS). The desired loci are then amplified from the extracted DNA via polymerase chain reaction (PCR). Fluorescently-labeled primers for 4-5 different loci are used per reaction, with 18 loci being amplified in a total of four reactions. The PCR products may be subjected to agarose gel electrophoresis to verify the

  8. DNA Fingerprinting of Mycobacterium leprae Strains Using Variable Number Tandem Repeat (VNTR) - Fragment Length Analysis (FLA)

    PubMed Central

    Jensen, Ronald W.; Rivest, Jason; Li, Wei; Vissa, Varalakshmi

    2011-01-01

    The study of the transmission of leprosy is particularly difficult since the causative agent, Mycobacterium leprae, cannot be cultured in the laboratory. The only sources of the bacteria are leprosy patients, and experimentally infected armadillos and nude mice. Thus, many of the methods used in modern epidemiology are not available for the study of leprosy. Despite an extensive global drug treatment program for leprosy implemented by the WHO1, leprosy remains endemic in many countries with approximately 250,000 new cases each year.2 The entire M. leprae genome has been mapped3,4 and many loci have been identified that have repeated segments of 2 or more base pairs (called micro- and minisatellites).5 Clinical strains of M. leprae may vary in the number of tandem repeated segments (short tandem repeats, STR) at many of these loci.5,6,7 Variable number tandem repeat (VNTR)5 analysis has been used to distinguish different strains of the leprosy bacilli. Some of the loci appear to be more stable than others, showing less variation in repeat numbers, while others seem to change more rapidly, sometimes in the same patient. While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing7,8,9, the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. Multiple locus VNTR analysis (MLVA)10 has been used to study leprosy evolution and transmission in several countries including China11,12, Malawi8, the Philippines10,13, and Brazil14. MLVA involves multiple steps. First, bacterial DNA is extracted along with host tissue DNA from clinical biopsies or slit skin smears (SSS).10 The desired loci are then amplified from the extracted DNA via polymerase chain reaction (PCR). Fluorescently-labeled primers for 4-5 different loci are used per reaction, with 18 loci being amplified in a total of four reactions.10 The PCR products may be subjected to agarose

  9. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

    PubMed Central

    Bilgin Sonay, Tugce; Carvalho, Tiago; Robinson, Mark D.; Greminger, Maja P.; Krützen, Michael; Comas, David; Highnam, Gareth; Mittelman, David; Sharp, Andrew; Marques-Bonet, Tomàs; Wagner, Andreas

    2015-01-01

    Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1–5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2–50 bp). Genes that contained TRs in the promoters, in their 3′ untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1–5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation. PMID:26290536

  10. Low speed test of the aft inlet designed for a tandem fan V/STOL nacelle

    NASA Technical Reports Server (NTRS)

    Rhoades, W. W.; Ybarra, A. H.

    1980-01-01

    An approximately .25 scale model of a Tandem Fan nacelle designed for a Type A V/STOL aircraft configuration was tested in a 10-by-10 foot wind tunnel. A 12 inch, tip driven, turbofan simulator was used to provide the suction source for the aft fan inlet. The front fan inlet was faired over for this test entry. Model variables consisted of a long aft inlet cowl, a short aft inlet cowl, a shaft simulator, blow-in door passages and diffuser vortex generators. Inlet pressure recovery, distortion, inlet angle of attack separation limits were evaluated at tunnel velocities from 0 to 240 knots, angles of attack from -10 to 40 degrees and inlet flow rates representative of throat Mach numbers of 0.1 to 0.6. High inlet performance and stable operation was verified at all design forward speed and angle of attack conditions. The short aft inlet configuration provided exceptionally high pressure recovery except at the highest combination of angle of attack and forward speed. The flow quality at the fan face was somewhat degraded by the addition of blow-in door passages to the long aft inlet configuration due to the pressure disturbances generated by the flow entering the diffuser through the auxiliary air passages.

  11. Identification of a novel cancer-specific immunodominant glycopeptide epitope in the MUC1 tandem repeat.

    PubMed

    Tarp, Mads A; Sørensen, Anne Louise; Mandel, Ulla; Paulsen, Hans; Burchell, Joy; Taylor-Papadimitriou, Joyce; Clausen, Henrik

    2007-02-01

    The cell membrane mucin MUC1 is over-expressed and aberrantly glycosylated in many cancers, and cancer-associated MUC1 glycoforms represent potential targets for immunodiagnostic and therapeutic measures. We have recently shown that MUC1 with GalNAcalpha1-O-Ser/Thr (Tn) and NeuAcalpha2-6GalNAcalpha1-O-Ser/Thr (STn) O-glycosylation is a cancer-specific glycoform, and that Tn/STn-MUC1 glycopeptide-based vaccines can override tolerance in human MUC1 transgenic mice and induce humoral immunity with high specificity for MUC1 cancer-specific glycoforms (Sorensen AL, Reis CA, Tarp MA, Mandel U, Ramachandran K, Sankaranarayanan V, Schwientek T, Graham R, Taylor-Papadimitriou J, Hollingsworth MA, et al. 2006. Chemoenzymatically synthesized multimeric Tn/STn MUC1 glycopeptides elicit cancer-specific anti-MUC1 antibody responses and override tolerance. Glycobiology. 16:96-107). In order to further characterize the immune response to Tn/STn-MUC1 glycoforms, we generated monoclonal antibodies with specificity similar to the polyclonal antibody response found in transgenic mice. In the present study, we define the immunodominant epitope on Tn/STn-MUC1 glycopeptides to the region including the amino acids GSTA of the MUC1 20-amino acid tandem repeat (HGVTSAPDTRPAPGSTAPPA). Most other MUC1 antibodies are directed to the PDTR region, although patients with antibodies to the GSTA region have been identified. A panel of other MUC1 glycoform-specific monoclonal antibodies was included for comparison. The study demonstrates that the GSTA region of the MUC1 tandem repeat contains a highly immunodominant epitope when presented with immature short O-glycans. The cancer-specific expression of this glycopeptide epitope makes it a prime candidate for immunodiagnostic and therapeutic measures.

  12. Pharmacokinetic properties of tandem d-peptides designed for treatment of Alzheimer's disease.

    PubMed

    Leithold, Leonie H E; Jiang, Nan; Post, Julia; Niemietz, Nicole; Schartmann, Elena; Ziehm, Tamar; Kutzsche, Janine; Shah, N Jon; Breitkreutz, Jörg; Langen, Karl-Josef; Willuweit, Antje; Willbold, Dieter

    2016-06-30

    Peptides are more and more considered for the development of drug candidates. However, they frequently exhibit severe disadvantages such as instability and unfavourable pharmacokinetic properties. Many peptides are rapidly cleared from the organism and oral bioavailabilities as well as in vivo half-lives often remain low. In contrast, some peptides consisting solely of d-enantiomeric amino acid residues were shown to combine promising therapeutic properties with high proteolytic stability and enhanced pharmacokinetic parameters. Recently, we have shown that D3 and RD2 have highly advantageous pharmacokinetic properties. Especially D3 has already proven promising properties suitable for treatment of Alzheimer's disease. Here, we analyse the pharmacokinetic profiles of D3D3 and RD2D3, which are head-to-tail tandem d-peptides built of D3 and its derivative RD2. Both D3D3 and RD2D3 show proteolytic stability in mouse plasma and organ homogenates for at least 24h and in murine and human liver microsomes for 4h. Notwithstanding their high affinity to plasma proteins, both peptides are taken up into the brain following i.v. as well as i.p. administration. Although both peptides contain identical d-amino acid residues, they are arranged in a different sequence order and the peptides show differences in pharmacokinetic properties. After i.p. administration RD2D3 exhibits lower plasma clearance and higher bioavailability than D3D3. We therefore concluded that the amino acid sequence of RD2 leads to more favourable pharmacokinetic properties within the tandem peptide, which underlines the importance of particular sequence motifs, even in short peptides, for the design of further therapeutic d-peptides. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Tandem Solar Cells from Solution-Processed CdTe and PbS Quantum Dots Using a ZnTe–ZnO Tunnel Junction

    DOE PAGES

    Crisp, Ryan W.; Pach, Gregory F.; Kurley, J. Matthew; ...

    2017-01-10

    We developed a monolithic CdTe-PbS tandem solar cell architecture in which both the CdTe and PbS absorber layers are solution-processed from nanocrystal inks. Due to their tunable nature, PbS quantum dots (QDs), with a controllable band gap between 0.4 and ~1.6 eV, are a promising candidate for a bottom absorber layer in tandem photovoltaics. In the detailed balance limit, the ideal configuration of a CdTe (Eg = 1.5 eV)-PbS tandem structure assumes infinite thickness of the absorber layers and requires the PbS band gap to be 0.75 eV to theoretically achieve a power conversion efficiency (PCE) of 45%. However, modelingmore » shows that by allowing the thickness of the CdTe layer to vary, a tandem with efficiency over 40% is achievable using bottom cell band gaps ranging from 0.68 and 1.16 eV. In a first step toward developing this technology, we explore CdTe-PbS tandem devices by developing a ZnTe-ZnO tunnel junction, which appropriately combines the two subcells in series. We examine the basic characteristics of the solar cells as a function of layer thickness and bottom-cell band gap and demonstrate open-circuit voltages in excess of 1.1 V with matched short circuit current density of 10 mA/cm2 in prototype devices.« less

  14. Study on limiting efficiencies of a-Si:H/μc-Si:H-based single-nanowire solar cells under single and tandem junction configurations

    NASA Astrophysics Data System (ADS)

    Zhai, Xiongfei; Cao, Guoyang; Wu, Shaolong; Shang, Aixue; Li, Xiaofeng

    2015-11-01

    Detailed balance calculations are presented for a-Si:H/μc-Si:H-based single- and tandem-junction single-nanowire solar cells (S- and T-SNSCs). Our study is based on three-dimensional finite-element electromagnetic simulation and thermodynamic balanced analysis, which includes radiative and Auger recombinations simultaneously. We quantify and compare the limiting short-circuit current densities, open-circuit voltages, and light-conversion efficiencies of these highly compact photovoltaic cells, addressing especially the effect of Auger recombination on the open-circuit voltages of SNSCs. Results show that tandem design leads to much higher light-conversion capability than μc-Si:H S-SNSCs, but exhibits superior performance than a-Si:H S-SNSCs only for cells with large radii.

  15. Study on limiting efficiencies of a-Si:H/μc-Si:H-based single-nanowire solar cells under single and tandem junction configurations

    SciTech Connect

    Zhai, Xiongfei; Cao, Guoyang; Wu, Shaolong E-mail: xfli@suda.edu.cn; Shang, Aixue; Li, Xiaofeng E-mail: xfli@suda.edu.cn

    2015-11-02

    Detailed balance calculations are presented for a-Si:H/μc-Si:H-based single- and tandem-junction single-nanowire solar cells (S- and T-SNSCs). Our study is based on three-dimensional finite-element electromagnetic simulation and thermodynamic balanced analysis, which includes radiative and Auger recombinations simultaneously. We quantify and compare the limiting short-circuit current densities, open-circuit voltages, and light-conversion efficiencies of these highly compact photovoltaic cells, addressing especially the effect of Auger recombination on the open-circuit voltages of SNSCs. Results show that tandem design leads to much higher light-conversion capability than μc-Si:H S-SNSCs, but exhibits superior performance than a-Si:H S-SNSCs only for cells with large radii.

  16. Summary of results from the Tandem Mirror Experiment (TMX)

    SciTech Connect

    Simonen, T.C.

    1981-02-26

    This report summarizes results from the successful experimental operation of the Tandem Mirror Experiment (TMX) over the period October 1978 through September 1980. The experimental program, summarized by the DOE milestones given in Table 1-1, had three basic phases: (1) an 8-month checkout period, October 1978 through May 1979; (2) a 6-month initial period of operation, June through November 1979, during which the basic principles of the tandem configuration were demonstrated (i.e., plasma confinement was improved over that of a single-cell mirror); and (3) a 10-month period, December 1979 through September 1980, during which the initial TMX results were corroborated by additional diagnostic measurements and many detailed physics investigations were carried out. This report summarizes the early results, presents results of recent data analysis, and outlines areas of ongoing research and data analysis which will be reported in future journal publications.

  17. Verification of automated peptide identifications from proteomic tandem mass spectra

    PubMed Central

    Tabb, David L; Friedman, David B; Ham, Amy-Joan L

    2010-01-01

    Shotgun proteomics yields tandem mass spectra of peptides that can be identified by database search algorithms. When only a few observed peptides suggest the presence of a protein, establishing the accuracy of the peptide identifications is necessary for accepting or rejecting the protein identification. In this protocol, we describe the properties of peptide identifications that can differentiate legitimately identified peptides from spurious ones. The chemistry of fragmentation, as embodied in the ‘mobile proton’ and ‘pathways in competition’ models, informs the process of confirming or rejecting each spectral match. Examples of ion-trap and tandem time-of-flight (TOF/TOF) mass spectra illustrate these principles of fragmentation. PMID:17406459

  18. Challenges and developments in tandem mass spectrometry based clinical metabolomics.

    PubMed

    Ceglarek, Uta; Leichtle, Alexander; Brügel, Mathias; Kortz, Linda; Brauer, Romy; Bresler, Kristin; Thiery, Joachim; Fiedler, Georg Martin

    2009-03-25

    'Clinical metabolomics' aims at evaluating and predicting health and disease risk in an individual by investigating metabolic signatures in body fluids or tissues, which are influenced by genetics, epigenetics, environmental exposures, diet, and behaviour. Powerful analytical techniques like liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) offers a rapid, effective and economical way to analyze metabolic alterations of pre-defined target metabolites in biological samples. Novel hyphenated technical approaches like the combination of tandem mass spectrometry combined with linear ion trap (QTrap mass spectrometry) combines both identification and quantification of known and unknown metabolic targets. We describe new concepts and developments of mass spectrometry based multi-target metabolome profiling in the field of clinical diagnostics and research. Particularly, the experiences from newborn screening provided important insights about the diagnostic potential of metabolite profiling arrays and directs to the clinical aim of predictive, preventive and personalized medicine by metabolomics.

  19. Marine Hydrokinetic Turbines operating in a streamwise tandem arrangement

    NASA Astrophysics Data System (ADS)

    Beninati, M. L.; Markovic, U. V.; Krane, M. H.

    2015-12-01

    A laboratory-scale study of the impact of separation distance on the performance of marine hydrokinetic turbines in a streamwise tandem arrangement is described. The study aims to give guidance concerning minimum, or optimal, turbine spacing in arrays. Testing was conducted in the hydraulic flume facility (9.8 m long, 1.2 m wide and 0.4 m deep) at Bucknell University. The devices were two-bladed model marine turbines with a rotor diameter of 0.1 m. For each separation distance, rotational speed of each device and velocity profiles of flow incident on the downstream turbine were measured. Results suggest limits for the minimum spacing between two turbines arranged in a tandem array.

  20. Protein identification using nano liquid chromatography-tandem mass spectrometry.

    PubMed

    Negroni, Luc

    2007-01-01

    Tandem mass spectrometry is an efficient technique for the identification of peptides on the basis of their fragmentation pattern (MS/MS scan). It can generate individual spectra for each peptide, thereby creating a powerful tool for protein identification on the basis of peptide characterization. This important advance in automatic data acquisition has allowed an efficient association between liquid chromatography and tandem mass spectrometry, and the use of nanocolumns and nanoelectrospray ionization has dramatically increased the efficiency of this method. Now large sets of peptides can be identified at a femtomole level. At the end of the process, batch processing of the MS/MS spectra produces peptide lists that identify purified proteins or protein mixtures with high confidence.